Biostar

9,156 results • Page 9 of 184

I'm having a problem visualizing a BAM file with IGV. The file was generated with bowtie2 + samtools and can be viewed normally with BamView. IGV, however, doesn...I'm having a problem visualizing a BAM file with IGV. The file was generated with bowtie2 + samtools and can be viewed normally with BamView. IGV, however, doesn&#39...with IGV as the one I used for alignment. I als…

IGV bam alignment

updated 9.2 years ago • novice

Hello, I have multiple .bam files from aligning reads via HISAT2. I would like to break up my bam file into single chromosome files utilizing R and then

R RNA-Seq bioconductor

updated 7.1 years ago • ddeemer

Hi Everyone, I'm trying to split a .bam file by a specific tag but am running into memory issues because the .bam file is position sorted and not tag sorted. I'd like

bamtools samtools sequencing

updated 7.8 years ago • Srw

Hi, I have a reference genome and reads from a cancer cell line aligned to that reference in a BAM and SAM file. I need to convert the BAM file into a FASTA file where the cancer consensus sequence is aligned to the reference...on BioStars addressing this question explain how to generate FASTQ and FASTA files based off the BAM file, but don't explain how to align those sequences to the reference…

BAM Assembly alignment FASTA SNP

updated 8.3 years ago • ryan.englander

I have a package (breakseq) that fails on newer versions of bam files. It uses older version of pysam which is unable to read the new bam file header. And throws errors. Is there an easy way...to convert .bam files from version 1.6 to 1.4

bam samtools

updated 2.0 years ago • Abhi

Hi. I'm trying to analyze a CAGE-seq data using CAGEr but I can not get pass the getCTSS command. The input is 8 single-end bam files (<210Mb). They are the result of mapping against Arabidopsis genome from TAIR10. Following the package vignette the data was loaded using, my.inputFiles <- list.files(bam.dir, pattern = "*.bam", recursive = TRUE, full.…

software error RNA-Seq

updated 4.9 years ago • SSL

cat qtrim1.fq qtrim2.fq single,fq > merged.fq ``` 4. Finally convert to bam: ``` java -jar picard.jar FastqToSam merged.fq O=trimmed_bam.bam SM=tumor ``` The resulting bam file is very small(~460Mb) as compared...suggest anything wrong or something you would have done differently. Number of reads in original bam: 1034838478 Number of reads in processed bam : 8053958

next-gen sequencing

updated 7.0 years ago • banerjeeshayantan

I have the following tasks that I need to carry out **a.** BAM mapping of Illumina HiSeq 4000 paired end 2*150bp reads to *de novo* assembly inferred from those reads, **b.** Sort BAM file by...coordinates, **c.** Index BAM file, **d.** Mark or Remove Duplicates in BAM file. When I was looking into software to generate my reads <=> assembly BAM file

BAM mapping

updated 7.3 years ago • Anand Rao

Hi I have a BAM file(s) which are reads aligned to reference genome.I'd like to know how can convert a BAM file to the full sequence in fasta...format, using the reads in the BAM file.I searched Biostars for BAM/SAM to FASTA conversion method, and found the two command could do this (Convert Bam File

next-gen software error

updated 7.4 years ago • rodbari.zahra

beside SAMTOOLS, PICARD or SAMBAMBA, is there any tool that you would recommend in order to sort a BAM based on read name ? It is a BAM file from EGA that contains cancer sequencing data, and when I do run PICARD SortSam, I am getting

bam sort

updated 6.7 years ago • Bogdan

I assembled an exome using the following command: bwa mem -t 12 -B 4 -O 6 -E 1 -M -R '@RG\tID:SRR1517898\tSM:HG00096\tPL:ILLUMINA' /home/ims.santos06/reference/hg38.fa /home/ims.santos06/fastq/SRR1517898_1.fastq.gz /home/ims.santos06/fastq/SRR1517898_2.fastq.gz | samtools view -1 - > /home/ims.santos06/bam/SRR1517`898.bam I received this mess…

Assembly alignment genome

updated 5.6 years ago • manubiomed20

Can vg stats -a be used on a bam file

stats vg

updated 19 months ago • idiaz026

for STAR aligner. But I have been trying to find a way to extract this information from the produced BAM file. I have looked through the internet for BAM to wiggle suggestions but have yet to find one that actually makes the same...wiggle file STAR outputs. I started exploring other solutions like BAM to bedgraph with step and bin sizes of 1. And the closest I have gotten to a solution is deep…

BAM SAM Wiggle

updated 4.7 years ago • dylan.t.fossl

synthetic) RNA reads to a self-made (short) reference sequence with bowtie2, and I have aquired the .bam file. Now I want to visualize this .bam file. I wanted to do this with IGV, however they want me to also provide a 'genome sequence...which I understood is the reference sequence). Isn't the reference sequence already provided in the .bam file? Why do I need to provide a reference sequence ag…

RNA bowtie2 IGV alignment BAM

updated 2.0 years ago • chrisgr

Hi all! I am trying to filter a BAM by chromosome using PySam. Using **Samtools**: samtools view -h mybam.bam 22 > mybam.bam.chr22.sam samtools view -bS mybam.bam.chr22.sam...return pysam.view("-bS", filtered_sam) # This doesn't seem to work What I want is to read the BAM, filter it out by chromosome but not saving the extra .sam/.bam files. Just read it, filter and the loop t…

Pysam BAM Python Samtools

updated 2.4 years ago • pablosolar.r

Hi folks -- haven't had much success in figuring this out through Googling. Hoping for some help here: My inputs are as follows: a BAM where each alignment has tags for a barcode and UMI. I also have an annotation file in .gff3 format. My desired output is a table...Hi folks -- haven't had much success in figuring this out through Googling. Hoping for some help here: My inputs are as follows: …

RNA-Seq BAM SAM annotation

updated 7.7 years ago • dzb

I have a BAM file containing an alignment to the GRCh38 "analysis pipeline" set with decoys (from ftp.ncbi.nlm.nih.gov/genbank/genomes...custom scripts. I want to run GATK indel realignment, base calibration, and variant calling on my BAM file using some of these remapped VCF files (e.g. `-known` on `RealignerTargetCreator`). The BAM and VCF come from different assemblies

genome next-gen

updated 4.0 years ago • dmyersturnbull

Hi, I am trying to convert a bam file to a bed file using R software however, I am currently unsuccessful. The below is what I have inputted so far in R-software...the package `bedtools` in R? What am I doing is it correct? Also, my goal is to combine more than 1 bam file together as I have 9 bam files and I would need to analyze the data holistically? Any suggestions? Thanks, A

updated 6.3 years ago • azzopardiannalise

genome (I'm using revised Cambridge reference sequence (NC_012920)). However, the resulting bam file is not in compressed format. The file extension is in .bam, but, I'm able to open it in a text editor. Here are the steps how...I got to this bam file. ``` #I'm using hisat2 to align fastq file to mitochondrial reference genome (I indexed it with hisat2). hisat2 -p 8 -x /home/user...SRR6423582_…

NGS samtools BAM

updated 2.3 years ago • Joshua

hello everyone! i am using this command samtools view -bh -F 2 FILE.bam mt > out.bam to get the discordant reads(one end aligns to mitochondria and the other to chromosome) and also those reads that align to (both ends) mitochondria only. out put file is a bam file. but when i want get fastq out of this bam file using command bamToFastq -i out.bam -fq out.1.fq -fq2 out.2.fq it shows…

samtools

updated 4.8 years ago • rehma.ar

Hello, I have four samples from the same condition (BAM files) and two controls (also BAM files). I want to eventually use plotHeatmap and plotProfile from deepTools, and I **dont** want...my questions are: 1. Is `bamCompare --operation mean` going to average the signal of the two input BAM files? There is no complete explanation about this option in the documentation... 2. Is this the best wa…

deepTools BAM bamCompare

updated 5.5 years ago • compuTE

I am running BAMboozle to anonymize variant sequences using the GRCh37 human reference genome on my bam files. How would I confirm that BAMboozle actually anonymized the bam files? Appreciate any help

BAMboozle

updated 21 months ago • mropri

Hello everybody! I can't visualize BAM files using IGV.... I have the BAM and BAI files but I can see nothing in the screen for IGV software. Could someone give me some

RNA-Seq

updated 2.2 years ago • friasoler

DNA_Seq_Variant_Calling_Pipeline/ to call variants. There is a step where the bam files are merged. I was wondering what the rationale behind merging the BAM files is

WES MergeSamFiles picard

updated 3.0 years ago • Thanh

Is there a way to calculate 5x, 10x, 20x, 30x coverage from a BAM file ? EDIT: I have a BAM file and I want to calculate the percentage of region of interest with 5x, 10x, 20x coverage. I used Samtools

coverage bam

updated 11.7 years ago • meredith19

assembly. I have different lib (of insert size) so i've mapped it separately, at the end I have a .bam file for each library: insert_size_350.bam insert_size_550.bam Now I would like to give it to BBmap pileup.sh for coverage...computation. But I think I have to merge the 2.bam files with : samtools merge output.bam *.bam I'm not sure, Is it the right way to do

bam contig coverage

updated 8.2 years ago • Picasa

Hi, I have a BAM file and a reference (let's say 1000 genomes data), I would like to extract from the BAM file all the possible overlapping bases

BAM Vcf

updated 8.0 years ago • Simo

I'm trying to merge different bam files with the same name (and, theoretically, the same sequence). They are the same set of libraries sequenced at two different...the matching pairs in order to simulate greater sequencing depth. I can do this just fine with two bams using `picard MergeSameFiles` or `samtools merge`, but the issue is that I have 96 bams in each folder. I'd like to do this progra…

bam sam samtools picard shell

updated 6.2 years ago • hylicase

I have two bam file for each sample which are paired end sequenced. I need to extract raw counts from these bam files which they look like...I founf these by a search but still don't know how to move forward as they are paired end and two bam files. featureCounts -T 4 -s 2 \ -a ~/annotations/Homo_sapiens.GRCh38.104.gtf \ -o ~/results/counts/s1_featurecounts.txt \ ~/results...…

featureCounts fastqc STAR samtools

updated 2.9 years ago • minoo

Hi, I have a bam file with vary reads length. I want to trim all the reads to the length of the shorter read in the file. I don't have access to...to the fastq files, and the bam files went through many filters, so I prefer to do the trimming on the bam. Any idea how cam I do it? Thanks

RNA-Seq genome sequencing next-gen

updated 5.2 years ago • rrapopor

Hi, I used Bedtools to convert BAM to BED format for my sequencing data. But together with BED I need the corresponding BIM and FAM files, which are not generated...option to convert such files but the input file should be PED and I couldnt find anyway to convert BAM to PED. It would be really helpful if anyone can suggest me a way for conversion of BAM to BED/BIM/FAM files. Thank you

bam bed format conversion

updated 13.1 years ago • Anjali

I managed to map SOLiD RNA-seq reads to a macaque genome assembly (macFas5). Now, I have 251 bam and bam.bai files to look into. I want to see whether there are any reads that map to a certain region on chromosome 11 and...I have to do it for all bam files I have. So, I was wondering if there is a more practical way to check this than zooming into the same region in each bam

RNA-Seq

updated 6.0 years ago • gokberk

I need to convert CRAM files to BAM files using [pysam][1]. I know from [this question][2] that converting a CRAM file to a BAM file requires the appropriate reference...at a different path. What I want to know is how I can use pysam to convert these CRAM files to BAM using the correct reference genome? I've seen code for converting CRAM to BAM in pysam that takes this form: `pysam.view(…

python pysam BAM CRAM

updated 6 months ago • sviatoslav.kendall

times: 1) ``` 227 Entering Passive Mode (193,62,192,8,185,217). [bam_header_read] invalid BAM binary header (this is not a BAM file). [main_samview] fail to read the header from "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp...2) ``` EOF marker is absent. The input is probably truncated. [bam_header_read] invalid BAM binary header (this is not a BAM file). [main_samview] fail to read the header fro…

bam samtools

updated 2.2 years ago • Maria333

hi all, we are creating an application and we want users to upload large BAM files. I was wondering if there are any recommendations for storing large files online. thanks

updated 11.1 years ago • win

Hi! Is their a way to know the genome build(ie., hg18 or hg19) to which the BAM file is aligned, other than manual inspection. Thank you

genomics chip-seq bam

updated 11.0 years ago • ChIP

Dear community, I am trying to convert BAM to FASTQ because the archived dataset is aligned to the older version of the reference genome. I need to realign to the...experience). I tried two different approaches and both of them show errors: Approach 1. Merge all BAM files into one (each BAM file represents alignment per chromosome). The error shows that some BAM files already exist and...asks…

samtools

updated 21 months ago • Qboy

I come up to aligning the fastq file based on the reference and as a result, I got the aligned bam file. For the next step, I am going to find an insertion sequence in the specific region of the bam file. Firstly, I checked the...I come up to aligning the fastq file based on the reference and as a result, I got the aligned bam file. For the next step, I am going to find an insertion sequence in t…

bam bwa

updated 2.3 years ago • kimpole1017

Hello, I would like to use Picard's CalculateHsMetrics to calculate per target coverage for Novaseq bam files. It seems that the tool is not able to calculate mean/normalized coverage for Novaseq bams but works well with Hiseq...bams. Novaseq bams report quality scores differently, therefore, my guess this is what is causing the issue. Do you have any suggestions

Picard

updated 3.5 years ago • genya35

Hi, I've been given a reference genome and BAM file(s) which are reads aligned to that reference. This will be the first time I've done anything with BAM/SAM formats. I&#39...d like to know how I would go about generating for each BAM file, the full sequence, using the reads in the BAM file and the reference they are aligned to, essentially resulting in a...FASTA format align…

BAM SAM R FASTA alignment

updated 10.1 years ago • ben.ward

lots of chrUn or decoy type contig. After alignment I would like to remove these reads from the bam but also remove any reference to these contig in the header (because it seems that just having these contig in the header...slows down some gatk tools). I had thought of ReorderSam but the problem is that it will sort the bam by coordinates, but for the rest, and in particular markduplicatespar…

filter header BAM

updated 3.7 years ago • quentin54520

Hi all, Anybody has the idea why redundant @SQ lines present in bam file header? I created the bam file by the following procedure: bowtie-build the genome create sam file using samtools by...aligning fastq files to the bowtie-build output convert sam to bam using samtools Those redundant files making error "Cannot add sequence that already exists in SAMSequenceDictionary

bowtie picard

updated 11.3 years ago • deepthithomaskannan

abundances in a sample. RSEM uses STAR to do the mapping (if asked) and optionally can output a BAM file where the reads are aligned against the genome and not the transcriptome (this genome file ends in .STAR.genome.bam...and is generated with the option "--star-output-genome-bam "). Now I was wondering, I want to use RSeQC to look at various quality related aspects of my BAM file, but which one…

RSEM STAR RSeQC BAM

updated 6.3 years ago • Freek

Hi guys, I would like to run bedtools multicov on paired (by name) .bam files and .bed files. In other words the situation is the following: > bedtools multicov -bams 1265_29_S1_L001_R1_001.sorted_PCRDuped.bam...gt; 1265_29_S1_L001_R1_001_q0.001_Counts.bed > bedtools multicov -bams 1265_30_S1_L001_R1_001.sorted_PCRDuped.bam -bed 1265_30_S1_L001_R1_001_q0.001broad_peaks.b…

ChIP-Seq bedtools

updated 4.9 years ago • elb

Hello All, Say I have 2 `BAM` files from 2 diploid reference genome(simulated maternal and paternal one). Now I need to extract the best reads alignments...from both the BAMs and merged into one` BAM` file. I have sorted both `Bam` files. I would like to know the best ways to proceed, at the end I need to...get the coverage of each variants from the `BAM` file. Any suggestion would be greatly …

RNA-Seq

updated 5.4 years ago • a.james

On can split a BAM by chromosome to speed up the processing of the BAMs. But it cannot be so simple: if two reads have been mapped on two distinct...some operations could lose some informations about the pair. So I suppose, I should create one extra bam file to save those pairs In the following operations what are the places where we can safely work on a given chromosome...recalibration Validat…

bam chromosome next-gen gatk picard

updated 12.4 years ago • Pierre Lindenbaum

Hello! I was about to re-run the mapping step to create BAM files with hg19 coordinates, but realised that perhaps it's easier to convert the existing GRCh37 BAM files to hg19 coordinates

GRCh37 hg19 BAM

updated 2.7 years ago • Joel Wallenius

for genes with correlating patterns. The thing is that for the RNA seq I used STAR to create the readcount files. I can create the readcount files for H3K27ac with htseq-count but I'm doubting if this is the right way to do...this (comparing readcounts obtained with 2 different methods). Would this be the right way to do this? And if not, could anyone give some advice

RNA-Seq ChIP-Seq STAR htseq-count readcounts

updated 8.8 years ago • thomasterTW

Hi there BioStars!, Given a bam file (from a set of analyzed ATACseq data), and a list of disease variants (in VCF format.), how can I determine if any "disease...Hi there BioStars!, Given a bam file (from a set of analyzed ATACseq data), and a list of disease variants (in VCF format.), how can I determine if any "disease variant...is present on my bam file? Many thanks in advance, Best, -M…

disease-variants VCF bam ATAC-seq

updated 22 months ago • masaver

EOF marker is absent. The input is probably truncated. [bam_header_read] invalid BAM binary header (this is not a BAM file). File cufflinks_frsecondstrand/cuffmerge/trout_cuffmerge/tmp/mergeSam_fileMhPT93...doesn't appear to be a valid BAM file, trying SAM... but it seems to complete ok, and produces a merged.gtf file at the end. Is this running correctly or is there...EOF marke…

RNA-Seq BAM cuffmerge error

updated 8.9 years ago • jenkelly

9,156 results • Page 9 of 184

Recent Votes

Answer: Understanding Re-use of Query Sequences in Long Read Alignments

Comment: SlingShot and Subsetting data

Reproducibility Crisis

Comment: Shotgun dataset with polyG, low qualiity

Comment: Batch effect or biological difference

Comment: Inconsistency between VCF and HGVS

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