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Comment: Comment: Error massage when running a GATK tool (selectvariants): no positional argument
17 months ago by mohsamir2016 ▴ 30
0
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1
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1.4k
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Comment: Comment: Error massage when running a GATK tool (selectvariants): no positional argument
17 months ago by mohsamir2016 ▴ 30
0
votes
5
replies
1.4k
views
Error message when running a GATK SelectVariants: no positional argument is defined for this tool
GATK SNPs
updated 17 months ago by 44k • written 17 months ago by ▴ 30
3
votes
11
replies
2.8k
views
6 follow
Getting sequences from fastq file using Grep command
Linux
updated 17 months ago by 14k • written 17 months ago by ▴ 30
0
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1
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2.8k
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Comment: Comment: Getting sequences from fastq file using Grep command
17 months ago by mohsamir2016 ▴ 30
0
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0
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2.8k
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Comment: Comment: Getting sequences from fastq file using Grep command
17 months ago by mohsamir2016 ▴ 30
0
votes
1
reply
2.8k
views
Comment: Comment: Getting sequences from fastq file using Grep command
17 months ago by mohsamir2016 ▴ 30
0
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0
replies
416
views
Correction for among sample/chromosomes for sequenicng depth, when comparing between samples or animals
GATK SNPs
17 months ago by mohsamir2016 ▴ 30
0
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1
reply
1.1k
views
Comment: Comment: How GATK pipeline called a homozygeous alternate allele (1/1) although one copy
updated 18 months ago by 44k • written 18 months ago by ▴ 30
0
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1
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1.1k
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Comment: Comment: How GATK pipeline called a homozygeous alternate allele (1/1) although one copy
18 months ago by mohsamir2016 ▴ 30
1
vote
7
replies
1.1k
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How GATK pipeline called a homozygeous alternate allele (1/1) although one copy is supported by 0 reads ?
SNP GATK
updated 18 months ago by 44k • written 18 months ago by ▴ 30
0
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1
reply
891
views
Comment: Comment: Extracting information from VCF file for many specific positions in specific chr
18 months ago by mohsamir2016 ▴ 30
0
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3
replies
891
views
Extracting information from VCF file for many specific positions in specific chromosomes
SNP RNA GATK seq
updated 18 months ago by 164k • written 18 months ago by ▴ 30
0
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1
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1.9k
views
Comment: Comment: Concatenating fastq for the same sample or doing it separately and merge at the
18 months ago by mohsamir2016 ▴ 30
1
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8
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1.9k
views
Concatenating fastq for the same sample or doing it separately and merge at the BAM stage ?
RNA-seq
updated 18 months ago by 44k • written 18 months ago by ▴ 30
0
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1
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3.6k
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Comment: Comment: bcftools isec output for multiple vcf files interpretations
19 months ago by mohsamir2016 ▴ 30
0
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0
replies
353
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Visualizing a mapped SNPs/INDELs on chromosomes of chicken
Genomic
19 months ago by mohsamir2016 ▴ 30
0
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1
reply
3.7k
views
Failed to install a package from Bioconductor and the library location not writable
Bioconductor RNA-seq R
updated 22 months ago by 44k • written 22 months ago by ▴ 30
0
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3
replies
1.6k
views
Does a merged VCF file (using bcftools merge) contain unique SNPs or INDELs from all merged VCF files
VCF
updated 23 months ago by ★ 2.3k • written 23 months ago by ▴ 30
0
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1
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1.6k
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Answer: Answer: Does a merged VCF file (using bcftools merge) contain unique SNPs or INDELs fro
23 months ago by mohsamir2016 ▴ 30
2
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2
replies
3.1k
views
How to add contigs name and length to the header of a VCF file ?
SNP RNA-seq GATK
updated 21 months ago by 44k • written 23 months ago by ▴ 30
0
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0
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3.1k
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Comment: Comment: How to add contigs name and length to the header of a VCF file ?
23 months ago by mohsamir2016 ▴ 30
0
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3
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1.6k
views
Which database to be used for (base quality score recalibration) for chicken ?
SNPs RNA-seq STAR
updated 23 months ago by ★ 2.3k • written 23 months ago by ▴ 30
0
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1
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1.6k
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Comment: Comment: Which database to be used for (base quality score recalibration) for chicken ?
23 months ago by mohsamir2016 ▴ 30
0
votes
0
replies
800
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How to get a SNPs file for chicken genome to be used for base-quality score recaliberation step of GATK variant calling
SNPs
23 months ago by mohsamir2016 ▴ 30
1
vote
5
replies
1.9k
views
Which threshold to be put in the MAPQ when doing mpileup of BCF tools on a STAR-generated BAM file ?
RNAseq STAR
updated 2.0 years ago by 6.2k • written 2.0 years ago by ▴ 30
0
votes
1
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1.9k
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Comment: Comment: Which threshold to be put in the MAPQ when doing mpileup of BCF tools on a STAR-
2.0 years ago by mohsamir2016 ▴ 30
0
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0
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1.9k
views
Comment: Comment: Which threshold to be put in the MAPQ when doing mpileup of BCF tools on a STAR-
2.0 years ago by mohsamir2016 ▴ 30
0
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0
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2.5k
views
Comment: Comment: Number of PCR duplicates in STAR-generated BAM file have no duplicate before and
2.0 years ago by mohsamir2016 ▴ 30
3
votes
8
replies
2.5k
views
Number of PCR duplicates in STAR-generated BAM file have no duplicate before and after fixmate/duplicate removal ?
RNA-seq STAR
updated 21 months ago by 44k • written 2.1 years ago by ▴ 30
0
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0
replies
2.5k
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Comment: Comment: Number of PCR duplicates in STAR-generated BAM file have no duplicate before and
2.1 years ago by mohsamir2016 ▴ 30
0
votes
1
reply
2.5k
views
Comment: Comment: Number of PCR duplicates in STAR-generated BAM file have no duplicate before and
2.1 years ago by mohsamir2016 ▴ 30
0
votes
0
replies
2.5k
views
Comment: Comment: Number of PCR duplicates in STAR-generated BAM file have no duplicate before and
2.1 years ago by mohsamir2016 ▴ 30
1
vote
12
replies
3.8k
views
Confused about % of mapped and unmapped reads output from STAR aligner
RNAseq STAR
updated 14 months ago by 44k • written 2.1 years ago by ▴ 30
0
votes
0
replies
3.8k
views
Comment: Comment: Confused about % of mapped and unmapped reads output from STAR aligner
2.1 years ago by mohsamir2016 ▴ 30
0
votes
1
reply
3.8k
views
Comment: Comment: Confused about % of mapped and unmapped reads output from STAR aligner
updated 2.1 years ago by 44k • written 2.1 years ago by ▴ 30
0
votes
0
replies
381
views
Better understanding of STAR statistical summary
RNA-seq STAR
updated 21 months ago by 44k • written 2.1 years ago by ▴ 30
0
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1
reply
3.8k
views
Comment: Comment: Confused about % of mapped and unmapped reads output from STAR aligner
2.1 years ago by mohsamir2016 ▴ 30
0
votes
1
reply
3.8k
views
Comment: Comment: Confused about % of mapped and unmapped reads output from STAR aligner
2.1 years ago by mohsamir2016 ▴ 30
0
votes
2
replies
3.8k
views
Comment: Comment: Confused about % of mapped and unmapped reads output from STAR aligner
2.1 years ago by mohsamir2016 ▴ 30
3
votes
7
replies
2.8k
views
Confused with output of STAR aligner for paired end reads and need advice on closely related SNPs analyses
RNA-seq
updated 21 months ago by 44k • written 2.1 years ago by ▴ 30
0
votes
2
replies
2.8k
views
Comment: Comment: Confused with output of STAR aligner for paired end reads and need advice on clo
updated 21 months ago by 44k • written 2.1 years ago by ▴ 30
0
votes
0
replies
2.8k
views
Comment: Comment: Confused with output of STAR aligner for paired end reads and need advice on clo
2.1 years ago by mohsamir2016 ▴ 30
0
votes
1
reply
2.8k
views
Comment: Comment: Confused with output of STAR aligner for paired end reads and need advice on clo
updated 21 months ago by 44k • written 2.1 years ago by ▴ 30
0
votes
1
reply
1.2k
views
How can I descending reorder the dots in the scatter plot in ggplot based on the X values ?
RNA seq
updated 2.2 years ago by ★ 1.8k • written 2.2 years ago by ▴ 30
4
votes
3
replies
850
views
Confused about which comparison to give a more accurate answer in RNA seq experimen t
RNA seq
updated 2.2 years ago by 14k • written 2.2 years ago by ▴ 30
0
votes
1
reply
850
views
Comment: Comment: Confused about which comparison to give a more accurate answer in RNA seq experi
2.2 years ago by mohsamir2016 ▴ 30
0
votes
0
replies
367
views
Should the least DE genes are the same as the ones with least tagwise dispersion in EdgeR ?
RNA seq
2.2 years ago by mohsamir2016 ▴ 30
0
votes
0
replies
404
views
Should the least DE genes are the same as the ones with least tagwise dispersion in EdgeR ?
edgeR RNA-seq
updated 2.3 years ago by 85k • written 2.3 years ago by ▴ 30
0
votes
2
replies
689
views
Plotting multiple genes across 4- species
RNA seq
updated 2.4 years ago by 14k • written 2.4 years ago by ▴ 30
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