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1
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Which threshold to be put in the MAPQ when doing mpileup of BCF tools on a STAR-generated BAM file ?
RNAseq STAR
updated 9 weeks ago by ▴ 910 • written 2.9 years ago by ▴ 30
0
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1
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2.0k
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Comment: Comment: Error massage when running a GATK tool (selectvariants): no positional argument
2.3 years ago by mohsamir2016 ▴ 30
0
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1
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2.0k
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Comment: Comment: Error massage when running a GATK tool (selectvariants): no positional argument
2.3 years ago by mohsamir2016 ▴ 30
0
votes
5
replies
2.0k
views
Error message when running a GATK SelectVariants: no positional argument is defined for this tool
GATK SNPs
updated 2.3 years ago by 45k • written 2.3 years ago by ▴ 30
4
votes
11
replies
5.1k
views
6 follow
Getting sequences from fastq file using Grep command
Linux
updated 2.3 years ago by 15k • written 2.3 years ago by ▴ 30
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1
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5.1k
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Comment: Comment: Getting sequences from fastq file using Grep command
2.3 years ago by mohsamir2016 ▴ 30
0
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0
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5.1k
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Comment: Comment: Getting sequences from fastq file using Grep command
2.3 years ago by mohsamir2016 ▴ 30
0
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1
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5.1k
views
Comment: Comment: Getting sequences from fastq file using Grep command
2.3 years ago by mohsamir2016 ▴ 30
0
votes
0
replies
542
views
Correction for among sample/chromosomes for sequenicng depth, when comparing between samples or animals
GATK SNPs
2.3 years ago by mohsamir2016 ▴ 30
0
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1
reply
1.5k
views
Comment: Comment: How GATK pipeline called a homozygeous alternate allele (1/1) although one copy
updated 2.4 years ago by 45k • written 2.4 years ago by ▴ 30
0
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1
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1.5k
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Comment: Comment: How GATK pipeline called a homozygeous alternate allele (1/1) although one copy
2.4 years ago by mohsamir2016 ▴ 30
1
vote
7
replies
1.5k
views
How GATK pipeline called a homozygeous alternate allele (1/1) although one copy is supported by 0 reads ?
SNP GATK
updated 2.4 years ago by 45k • written 2.4 years ago by ▴ 30
0
votes
1
reply
1.2k
views
Comment: Comment: Extracting information from VCF file for many specific positions in specific chr
2.4 years ago by mohsamir2016 ▴ 30
0
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3
replies
1.2k
views
Extracting information from VCF file for many specific positions in specific chromosomes
SNP RNA GATK seq
updated 2.4 years ago by 166k • written 2.4 years ago by ▴ 30
0
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1
reply
3.0k
views
Comment: Comment: Concatenating fastq for the same sample or doing it separately and merge at the
2.4 years ago by mohsamir2016 ▴ 30
1
vote
8
replies
3.0k
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Concatenating fastq for the same sample or doing it separately and merge at the BAM stage ?
RNA-seq
updated 2.4 years ago by 45k • written 2.4 years ago by ▴ 30
0
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1
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5.0k
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Comment: Comment: bcftools isec output for multiple vcf files interpretations
2.5 years ago by mohsamir2016 ▴ 30
0
votes
0
replies
552
views
Visualizing a mapped SNPs/INDELs on chromosomes of chicken
Genomic
2.5 years ago by mohsamir2016 ▴ 30
0
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1
reply
5.6k
views
Failed to install a package from Bioconductor and the library location not writable
Bioconductor RNA-seq R
updated 2.7 years ago by 45k • written 2.7 years ago by ▴ 30
0
votes
3
replies
2.2k
views
Does a merged VCF file (using bcftools merge) contain unique SNPs or INDELs from all merged VCF files
VCF
updated 2.7 years ago by ★ 2.4k • written 2.7 years ago by ▴ 30
0
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1
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2.2k
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Answer: Answer: Does a merged VCF file (using bcftools merge) contain unique SNPs or INDELs fro
2.7 years ago by mohsamir2016 ▴ 30
2
votes
2
replies
4.2k
views
How to add contigs name and length to the header of a VCF file ?
SNP RNA-seq GATK
updated 2.7 years ago by 45k • written 2.8 years ago by ▴ 30
0
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0
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4.2k
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Comment: Comment: How to add contigs name and length to the header of a VCF file ?
2.8 years ago by mohsamir2016 ▴ 30
0
votes
3
replies
2.0k
views
Which database to be used for (base quality score recalibration) for chicken ?
SNPs RNA-seq STAR
updated 2.8 years ago by ★ 2.4k • written 2.8 years ago by ▴ 30
0
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1
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2.0k
views
Comment: Comment: Which database to be used for (base quality score recalibration) for chicken ?
2.8 years ago by mohsamir2016 ▴ 30
0
votes
0
replies
910
views
How to get a SNPs file for chicken genome to be used for base-quality score recaliberation step of GATK variant calling
SNPs
2.8 years ago by mohsamir2016 ▴ 30
0
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1
reply
3.4k
views
Comment: Comment: Which threshold to be put in the MAPQ when doing mpileup of BCF tools on a STAR-
2.9 years ago by mohsamir2016 ▴ 30
0
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0
replies
3.4k
views
Comment: Comment: Which threshold to be put in the MAPQ when doing mpileup of BCF tools on a STAR-
2.9 years ago by mohsamir2016 ▴ 30
0
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0
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3.3k
views
Comment: Comment: Number of PCR duplicates in STAR-generated BAM file have no duplicate before and
2.9 years ago by mohsamir2016 ▴ 30
3
votes
8
replies
3.3k
views
Number of PCR duplicates in STAR-generated BAM file have no duplicate before and after fixmate/duplicate removal ?
RNA-seq STAR
updated 2.7 years ago by 45k • written 2.9 years ago by ▴ 30
0
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0
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3.3k
views
Comment: Comment: Number of PCR duplicates in STAR-generated BAM file have no duplicate before and
2.9 years ago by mohsamir2016 ▴ 30
0
votes
1
reply
3.3k
views
Comment: Comment: Number of PCR duplicates in STAR-generated BAM file have no duplicate before and
2.9 years ago by mohsamir2016 ▴ 30
0
votes
0
replies
3.3k
views
Comment: Comment: Number of PCR duplicates in STAR-generated BAM file have no duplicate before and
2.9 years ago by mohsamir2016 ▴ 30
1
vote
12
replies
5.4k
views
Confused about % of mapped and unmapped reads output from STAR aligner
RNAseq STAR
updated 2.1 years ago by 45k • written 2.9 years ago by ▴ 30
0
votes
0
replies
5.4k
views
Comment: Comment: Confused about % of mapped and unmapped reads output from STAR aligner
2.9 years ago by mohsamir2016 ▴ 30
0
votes
1
reply
5.4k
views
Comment: Comment: Confused about % of mapped and unmapped reads output from STAR aligner
updated 2.9 years ago by 45k • written 2.9 years ago by ▴ 30
0
votes
0
replies
498
views
Better understanding of STAR statistical summary
RNA-seq STAR
updated 2.7 years ago by 45k • written 2.9 years ago by ▴ 30
0
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1
reply
5.4k
views
Comment: Comment: Confused about % of mapped and unmapped reads output from STAR aligner
2.9 years ago by mohsamir2016 ▴ 30
0
votes
1
reply
5.4k
views
Comment: Comment: Confused about % of mapped and unmapped reads output from STAR aligner
2.9 years ago by mohsamir2016 ▴ 30
0
votes
2
replies
5.4k
views
Comment: Comment: Confused about % of mapped and unmapped reads output from STAR aligner
2.9 years ago by mohsamir2016 ▴ 30
3
votes
9
replies
4.0k
views
Confused with output of STAR aligner for paired end reads and need advice on closely related SNPs analyses
RNA-seq
updated 11 weeks ago by 154k • written 3.0 years ago by ▴ 30
0
votes
2
replies
4.0k
views
Comment: Comment: Confused with output of STAR aligner for paired end reads and need advice on clo
updated 2.7 years ago by 45k • written 3.0 years ago by ▴ 30
0
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0
replies
4.0k
views
Comment: Comment: Confused with output of STAR aligner for paired end reads and need advice on clo
3.0 years ago by mohsamir2016 ▴ 30
0
votes
1
reply
4.0k
views
Comment: Comment: Confused with output of STAR aligner for paired end reads and need advice on clo
updated 2.7 years ago by 45k • written 3.0 years ago by ▴ 30
0
votes
1
reply
2.0k
views
How can I descending reorder the dots in the scatter plot in ggplot based on the X values ?
RNA seq
updated 3.0 years ago by ★ 1.9k • written 3.0 years ago by ▴ 30
4
votes
3
replies
1.2k
views
Confused about which comparison to give a more accurate answer in RNA seq experimen t
RNA seq
updated 3.1 years ago by 15k • written 3.1 years ago by ▴ 30
0
votes
1
reply
1.2k
views
Comment: Comment: Confused about which comparison to give a more accurate answer in RNA seq experi
3.1 years ago by mohsamir2016 ▴ 30
0
votes
0
replies
520
views
Should the least DE genes are the same as the ones with least tagwise dispersion in EdgeR ?
RNA seq
3.1 years ago by mohsamir2016 ▴ 30
0
votes
0
replies
528
views
Should the least DE genes are the same as the ones with least tagwise dispersion in EdgeR ?
edgeR RNA-seq
updated 3.2 years ago by 89k • written 3.2 years ago by ▴ 30
0
votes
2
replies
905
views
Plotting multiple genes across 4- species
RNA seq
updated 3.2 years ago by 15k • written 3.2 years ago by ▴ 30
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