Biostar

9,149 results • Page 7 of 183

Hi, I'm currently writing a script in python that will read in both FASTA and BAM files and output certain information. Right now I'm in need of a BAM file and matching FASTA file to play around with. As most...BAM files are huge, for eg.the human genome, I though it would be good to play around with a yeast strain. I have the necessary FASTA...http://hgdownload.cse.ucsc.edu/goldenPath/sacCer2/…

S. Cerevisiae BAM FASTA Sequencing Alignment

updated 8.1 years ago • AlchemistMoz

my RNA-seq PE on Transcriptome with no gtf file available using Bowtie2. Used Samtools to make bam files and sorted. Used sambamba merge to merge the sorted bam replicates and resorted using samtools. bowtie2 -x ../refrence

RNA-Seq R bowtie2 samtools Hisat2

updated 6.4 years ago • Shahzad

genome downloaded from UCSC). However, I noted that the BED file coordinate is 0-based, while the BAM file used by `bedtools multicov` was sorted by samtools and its coordinate was 1-based. So, do I need to transform the coordinate...of the BAM file from 1-based to 0-based before run the `bedtools multicov` command? Thank you

RNA-Seq alignment genome

updated 7.4 years ago • yuabrahamliu

I have used samtools to make bam files and it is perfectly showing the data in igv. somehow I am unable to get the counts when using htseq. after going through...literature I think I needed to **sort bam files according to coordinates**. is there anyone can **share a command example** that how a sorted bam can be generated using...samtools. thanks ps. currently is gives an empty txt file when I…

next-gen-sequencing gene rna-seq

updated 21 months ago • Shahzad

Hi guys, I have a folder with around 300 `.bam` files. Each `.bam` file is a lane of a sample and hence 4 lanes make a sample. I would like to merge the .bam files of the four lanes...me please? The line I use to merge normally is the following: samtools merge S1_merged.bam *bam Thank you in advance

bam samtools RNA-Seq

updated 6.7 years ago • elb

Hi all, Let's say I have SAM/BAM files containing single-end reads. My reads look like: Intron 1 - Exon 2 - Intron 2 - Exon 3 - Intron 3 My aim is to get rid of all intron...sequences so that my reads will look like: Exon 2 - Exon 3 I intend to split BAM files into two BAM files based on the region. One BAM file contains exon 2 sequences and the other contains exon 3. Then, re...merge split BA…

next-gen alignment sequence

updated 8.5 years ago • KT

Dear All, I am using BAM files for chip-seq analysis. The chromosome notation in a usual BAM file is like: chr1. In my file the chromosomme notation...is 1. Is there a way to change that in the BAM file? For further analysis it is very important to change the notation. Many thanks! Greetz Lisanne

samtools bam

updated 4.8 years ago • Lisanne

hello my friends; I have a question: I have two sample .bam file from illumina for my patient, now I want to know if i convert this two file to bed file, does any different between two

sequencing

updated 5.3 years ago • mahdi_sh1387

Hi, I've a little question on sam and bam file sizes. When I use bwa on paired-end reads (~50M reads) on a small reference sequence (~100 kb) , I've a bam file of about 5 Go . After...500 reads max) But When I use tophat with the same input and the same reference, the output bam has a size of only 10 kb and the number of aligned reads is the same... So is it a way to reduce my bam file ? Tha…

bam sam

updated 13.0 years ago • Nicolas Rosewick

I'd like to rename (sample name) a BAM file. What is the easiest way to do this

bam

updated 13 months ago • 8armed

I have build a web based RNA-Seq analysis platform and It has run successfully. However, I have no bam file of transcriptome to test my platform. Where can I find some bam files which have been released? Thanks

bam RNA-seq

updated 2.1 years ago • snakesgun

Hello, I have been working on this bam file to visualize the alignment, and till now I have not achieved any sort of result, can anyone help me with this issue? I...Hello, I have been working on this bam file to visualize the alignment, and till now I have not achieved any sort of result, can anyone help me with this issue? I am...working on metagenomics data, and trying to use samtools for visua…

Assembly genome next-gen

updated 5.1 years ago • vishalchanda364

Hi Biostars, Is it possible to visualize only the subset of reads from a bam file using IGV? Thanks, EDIT: Let's try to find completely universal way of doing this: Is it possible to visualize only the...subset of reads (1 mln random reads) from a bam file using IGV

IGV bam

updated 7.5 years ago • grant.hovhannisyan

I was trying to subsample WES BAM files with samtools view -s on coverage 75. My samples had mean coverage in target regions 195 and 130 so I used fractions...around 65-68. What I did wrong? If you have any ideas of other tools how to effectively subsample BAMs on the same number of reads or on the same coverage, please let me know

BAM sampling

updated 4.1 years ago • esimonova.me

Can someone guide me on how we can find heterozygous sites given a germline BAM file? (preferably in R) Basically, I would like to know the heterozygous sites in the germline BAM and then, using the reads...data from the tumor BAM file, look for those reads containing both a heterozygous location and a mutation. Thanks

R SNP next-gen-sequencing cancer

updated 2.6 years ago • marki

Hello everyone! So I was wondering if anyone had any advice or tools to help make different BAM or SAM files equivalent. What I mean by that is I have aligned the sequence data of different populations of a species to...Hello everyone! So I was wondering if anyone had any advice or tools to help make different BAM or SAM files equivalent. What I mean by that is I have aligned the sequence data …

alignment BAM SAM popoolation popoolation2

updated 4.8 years ago • keturner123

the reads against a reference genome (closely related to the sequenced Bacteria). Now I have the bam file. I plan on using Prokka to annotate my data. I believe Prokka doesnot take in a bam file for annotation purpose. What should...I do further? Should I extract a consensus sequence from the bam file? If so How should I proceed and if wrong, how will I proceed? Also how to get gene information i…

Assembly SNP sequencing genome alignment

updated 2.7 years ago • alok.helix

Dear all, I have easy script in bash using awk language. I filtrate bam file by GC content (see at code), but I need to get on output bam file too with header. Could you help me with this? thank you My code...Dear all, I have easy script in bash using awk language. I filtrate bam file by GC content (see at code), but I need to get on output bam file too with header. Could you help me with this? t…

header samtools BAM filtration

updated 3.4 years ago • filipzembol

I'm working with TCGA WGS BAMs through the Google Cloud Platform, and I've seen that there are files where the barcode is identical, but there is an additional...number appended to the filename before the .bam extension. For example, G32450.TCGA-FD-A3N5-01A-11D-A21A-08.1.bam G32450.TCGA-FD-A3N5-01A-11D-A21A-08.3.bam G32450.TCGA...08.2.bam G32450.TCGA-FD-A3N5-10A-01D-A21A-08.4.bam Do these c…

data bam cancer

updated 6.5 years ago • lucas.lochovsky

How can I tell if my BAM file is in BAM(SE) or BAMPE format? Does samtools have a command to help with this

BAM BAMPE BWA

updated 8.0 years ago • cpak1981

Hi, I have a bam file includes a single gene sequence with huge coverage (> 5000X) from which I want to call snps. I have several snps previously...identified in my sample which I am going to use as control to test my pipeline. From my original bam file , I want to generate some bam files with different coverage. Then I will call SNPs from each one of them, compare them with

bam filter SNPs caller

updated 6.6 years ago • tarek.mohamed

I need help with visualising a .bam file. So, what I did up to now was: I had one `.fastq` of 3.9 MB file containing many reads generated by Metrichor (I am sequencing...ngmlr -t 4 -r ref.fasta -q reads.fastq -o test.sam -x ont I converted this `.sam` file to a `.bam` file using `samtools`. I got a `.bam` file of 2 MB. The command I used was: samtools view -bT ref.fasta test.sam > …

alignment bam igv

updated 6.8 years ago • francois

Hello. I am new in genetics and I am interested in detection of mosaic genome from BAM file. I have my WGS 30x results. Is it possible to use it for mosaic detection even when samples were taken from only a single...location (mouth swab)? Are there any tools to detect it from BAM file? Thanks. Monika

BAM Mosaic WGS

updated 15 months ago • monkun84

Hey Guys, I'm quite new to bioinformatics and i've been struggling to work with large bam files (80Gb) for the last few weeks. Can anyone tell me if it is possible to split these bam files into smaller ones by chromosomal

bam galaxy

updated 13.1 years ago • Leandro Batista

from EGA (with the authors permissions of course), but noticed that the files are multiplexed bam files (HiSeq whole genome, HiSeq whole exome, RNASeq.) What is the easiest way to merge the multiplexed bam files? Thank you

bam multiplex

updated 10.3 years ago • Nikleotide

I found that in the ENCODE database, hg19 v19 contain two bam files for each biological replicate, and they are different bam file, so what is the difference between the two bam file

encode bam assembly

updated 8.8 years ago • li487

Hi! I have a paired end bam file and used bedtools to convert it to bed format (paired end). From this bed file I want to make a new bam file from the start...pos of read 1 and end pos of read 2. I already tried using bedtools bed to bam (using mouse genome file) but it seems that the output is incorrect. Thanks

BAM

updated 17 months ago • genomics_student

I was doing mitochondrial analysis using Gatk, in that they first converted bam file to unmapped and then converted it to fastq files for further processing. So is it necessary to convert the bam to ubam...before converting it to fastq files? If yes, then why? Does it makes any difference if we convert bam to fastq

fastq unmapped bam

updated 2.2 years ago • NikhilP

I have some large bam files for a pipeline. But the RAM ran out when I was performing the pipe. Sorting bam will cause fatal bugs to my pipeline and...RAM cannot be done for now due to the high expense). Then I thought I could split the original bam to several smaller bam files. But I cannot skip the sorting step. E.g. `samtools view` requires sorting and indexing before

samtools BAM bamtools

updated 2.4 years ago • tomas4482

Hi! I have three aligned pair end reads in BAM format. Two of them are of same sample run in different lanes. I first merged the files from same sample with read groups...Hi! I have three aligned pair end reads in BAM format. Two of them are of same sample run in different lanes. I first merged the files from same sample with read groups and...added read group to third one separately. After tha…

bam samtools merge

updated 12.6 years ago • lyfsa

From a .bam file of RNA sequence reads that are aligned to a mouse reference genome, how can I get a new bam file that contains this same...need to get one long read sequence for each location and not many reads like it's the case with this .bam file. For bases that in some reads (and not all) they seem to be mutated compared to reference, I need to have the most "probable

bam RNA-Seq genome assembly sequence

updated 5.5 years ago • Triple Nipple

I was trying to run CrossMap for a set of bam files using this script. But its showing error. ``` bam_list <- list.files(path = "home_hg19_Bam/", pattern = ".bam$", full.names=T) for...i in 1:length(bam_list)){ system(paste0("CrossMap.py bam ./hg18ToHg19.over.chain.gz", bam_list[i], folder, "home/SCLC_hg19_Bam/" ,gsub(".bam", "", bam_list[i]), "_hg19.bam

genome Assembly R

updated 3.1 years ago • ifudontmind_plzz

Hi, Is there a samtools or other tool command that given a bam (and/or indexed bam) file will report the number of sites sequenced

bam samtools RNA-Seq

updated 7.9 years ago • rubic

Hi all, what SAM/BAM viewer are you using? do you have any suggestion on a good BAM/SAM viewer? Thanks in advanced

viewer sam bam

updated 4.0 years ago • Ken

creating. However, in writing this script I've been using `samtools view -s` to sample the generated BAM files (one BAM that acts as the contaminate and one that acts as the base). I was running into problems where the final merged...Generate synthetic reads for the Base and contaminate fasta (this includes most importantly the BAM file). - Count the reads of both BAM files. - Using the read coun…

samtools BAM

updated 21 months ago • matt81rd

Hello, I have two questions regarding merging the `BAM` files. I have several libraries 4 lanes each. I demultiplexed, mapped against the reference genome, gave the read group...library=["Bob", "John"] (LIBRARIES, SAMPLES)=glob_wildcards("path/to/{library}_1_{sample}.bam") rule all: input: expand("{library}_{sample}.merged.bam", library=LIBRARIES, sample=SAMPLES…

samtools snakemake bam

updated 4.6 years ago • User000

Hello, I want to ask you what is the best way for visualizing big file (Bam), I am going to sort bam file with samtools sort at first, then convert it to bedgraph by this command: bedtools genomecov -ibam...bam -bg -scale 10.0, and visualize it by IGV. this way is right and certain in your idea or what else? thanks in advance

RNA-Seq bam visualize

updated 6.6 years ago • lkianmehr

Hello Biostars! Today I am trying to find a general approach that can be used on BAMs to normalise among each other. More specifically, I am trying to subtract the read alignment of control from sample alignment

next-gen Assembly ChIP-Seq

updated 7.4 years ago • anu014

I ran the following the command to extract bam file for specific chromosomal locus. samtools view -h accepted_hits.bam "EQ963475:334376-335722">AFLA_105440.bam...EQ963477 LN:2388123 @SQ SN:EQ963478 LN:2337902 ``` When I ran the below command for conversion of bam to fastq samtools bam2fq AFLA_105440.bam >AFLA_105440.fq it showing error like this: ``` [bam_header_read] E…

RNA-Seq

updated 23 months ago • Bioblazer

and do alignment with STAR and run STAR-Fusion. Everything looks good until I try to reverse the BAM files generated from STAR originally to fastq and rerun STAR-Fusion; this resulted in about half the fusions that as originally...called. So making a mistake somewhere when converting from BAM to fastq. So far I tried several tools including samtools fastq, picard RevertSam to a ubam and then…

RNA-Seq BAM sequencing

updated 6.3 years ago • simplitia

Hello, I have indexed my bam files as: > samtools index -b file.bam I get as a result a file.bam.bai. But when I try to convert it to BigWig with bamCoverage...E::hts_open_format] fail to open file 'file.bam.bai' The file file.bam.bai does not have BAM format The error persists if I change the file name to file.bam.bai. I checked with samtools flagstat, and I get the same...…

bigwig samtools index bamCoverage bai

updated 6.1 years ago • compuTE

Hi! I am building a program in java and part of it would be creating and handling BAM files. My problem is the following: before writing I would like to check if a BAM file with the same name already exists and...Hi! I am building a program in java and part of it would be creating and handling BAM files. My problem is the following: before writing I would like to check if a BAM file with the sa…

bam java

updated 8 months ago • Bertalan_Takacs

Hi all, I need to read bam file in my project. I met a problem. According to sam file format, the first information of bam file is: `char[4]` which is `BAM\1`. But

sequencing

updated 3.3 years ago • tianlq

Hello. I am fairly new to bioinformatics. I want to merge quite a few BAM files resulted from TopHat alignments. So I can play with them easier (as I don't have a lot of storage space) i cut them by the...region of interest. So now I only have around 10kb per BAM file. I am not sure how to correctly merge BAM files with samtools (in Linux). Do I have to change the headers? More specifically

RNA-Seq

updated 5.9 years ago • Sammy

Hi, Is there a straight forward way to call variants from aligned BAM file only for the mitochondrial chromosome? Thanks

MT variant calling assembly

updated 4.8 years ago • igorm

Hello! Can you suggest any way to convert fastq file to bam file? thx in advance

fastq bam

updated 4.2 years ago • arianc

Hello, I have a library of several hundred BAM files containing Y-sequences aligned to hg19. Now, since all major Y-players, like FTDNA, FGC, ISOGG, YBrowse... upgraded to hg38...my BAM files are pretty much useless since the SNP coordinates are according to hg38. Is there any way to convert these BAM files

alignment sequence

updated 7.4 years ago • kumbarov

Hi ! I made bam file and pileup file by using samtools, and I deleted this bam file because of its size. However, I found that I need to get some...about my data such as number of reads. Therefore, I want to ask (1) Can I reconstruct fastq or bam file from pileup file? or (2) Can I get some information related to mapped reads data from pileup file? Thanks

alignment bam mpileup samtools

updated 5.5 years ago • SSK

I am relatively new to the programs that analyze bam files. I am wondering if there is a program that allows us to have an alignment report of all the reads of a particular nucleotide...from the bam file? For example: chr1:2876597 Total read: 130 A: 120 T: 0 G: 8 C: 0 N: 0 Del: 2 Ins: 0 I have over 200 bam files and I would like to have a report

alignment bam

updated 7.8 years ago • kin182

Hi guys, I am aligning RNA-seq data using STAR and will need in later steps to use sorted BAM files. I was wondering what people suggest to use for BAM sorting? The options that I have considerer/used include: - `STAR --outSAMtype...BAM SortedByCoordinate` - but this crashes because of memory (we only have 128GB of RAM our server). That is when I'm merging lanes...This is fixable by limiting R…

RNA-Seq samtools STAR

updated 2.0 years ago • Kirill Tsyganov

9,149 results • Page 7 of 183

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