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Comment: Comment: Error massage when running a GATK tool (selectvariants): no positional argument
10 months ago by mohsamir2016 ▴ 30
0
votes
1
reply
980
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Comment: Comment: Error massage when running a GATK tool (selectvariants): no positional argument
10 months ago by mohsamir2016 ▴ 30
0
votes
5
replies
980
views
Error message when running a GATK SelectVariants: no positional argument is defined for this tool
GATK SNPs
updated 10 months ago by 43k • written 10 months ago by ▴ 30
3
votes
11
replies
1.8k
views
6 follow
Getting sequences from fastq file using Grep command
Linux
updated 10 months ago by 14k • written 10 months ago by ▴ 30
0
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1
reply
1.8k
views
Comment: Comment: Getting sequences from fastq file using Grep command
10 months ago by mohsamir2016 ▴ 30
0
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0
replies
1.8k
views
Comment: Comment: Getting sequences from fastq file using Grep command
10 months ago by mohsamir2016 ▴ 30
0
votes
1
reply
1.8k
views
Comment: Comment: Getting sequences from fastq file using Grep command
10 months ago by mohsamir2016 ▴ 30
0
votes
0
replies
355
views
Correction for among sample/chromosomes for sequenicng depth, when comparing between samples or animals
GATK SNPs
10 months ago by mohsamir2016 ▴ 30
0
votes
1
reply
884
views
Comment: Comment: How GATK pipeline called a homozygeous alternate allele (1/1) although one copy
updated 10 months ago by 43k • written 10 months ago by ▴ 30
0
votes
1
reply
884
views
Comment: Comment: How GATK pipeline called a homozygeous alternate allele (1/1) although one copy
10 months ago by mohsamir2016 ▴ 30
1
vote
7
replies
884
views
How GATK pipeline called a homozygeous alternate allele (1/1) although one copy is supported by 0 reads ?
SNP GATK
updated 10 months ago by 43k • written 10 months ago by ▴ 30
0
votes
1
reply
702
views
Comment: Comment: Extracting information from VCF file for many specific positions in specific chr
11 months ago by mohsamir2016 ▴ 30
0
votes
3
replies
702
views
Extracting information from VCF file for many specific positions in specific chromosomes
SNP RNA GATK seq
updated 11 months ago by 161k • written 11 months ago by ▴ 30
0
votes
1
reply
1.2k
views
Comment: Comment: Concatenating fastq for the same sample or doing it separately and merge at the
11 months ago by mohsamir2016 ▴ 30
1
vote
8
replies
1.2k
views
Concatenating fastq for the same sample or doing it separately and merge at the BAM stage ?
RNA-seq
updated 11 months ago by 43k • written 11 months ago by ▴ 30
0
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1
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2.4k
views
Comment: Comment: bcftools isec output for multiple vcf files interpretations
12 months ago by mohsamir2016 ▴ 30
0
votes
0
replies
278
views
Visualizing a mapped SNPs/INDELs on chromosomes of chicken
Genomic
12 months ago by mohsamir2016 ▴ 30
0
votes
1
reply
2.7k
views
Failed to install a package from Bioconductor and the library location not writable
Bioconductor RNA-seq R
updated 15 months ago by 43k • written 15 months ago by ▴ 30
0
votes
3
replies
1.3k
views
Does a merged VCF file (using bcftools merge) contain unique SNPs or INDELs from all merged VCF files
VCF
updated 15 months ago by ★ 2.1k • written 15 months ago by ▴ 30
0
votes
1
reply
1.3k
views
Answer: Answer: Does a merged VCF file (using bcftools merge) contain unique SNPs or INDELs fro
15 months ago by mohsamir2016 ▴ 30
2
votes
2
replies
2.4k
views
How to add contigs name and length to the header of a VCF file ?
SNP RNA-seq GATK
updated 14 months ago by 43k • written 16 months ago by ▴ 30
0
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0
replies
2.4k
views
Comment: Comment: How to add contigs name and length to the header of a VCF file ?
16 months ago by mohsamir2016 ▴ 30
0
votes
3
replies
1.4k
views
Which database to be used for (base quality score recalibration) for chicken ?
SNPs RNA-seq STAR
updated 16 months ago by ★ 2.1k • written 16 months ago by ▴ 30
0
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1
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1.4k
views
Comment: Comment: Which database to be used for (base quality score recalibration) for chicken ?
16 months ago by mohsamir2016 ▴ 30
0
votes
0
replies
733
views
How to get a SNPs file for chicken genome to be used for base-quality score recaliberation step of GATK variant calling
SNPs
16 months ago by mohsamir2016 ▴ 30
1
vote
5
replies
1.5k
views
Which threshold to be put in the MAPQ when doing mpileup of BCF tools on a STAR-generated BAM file ?
RNAseq STAR
updated 17 months ago by 6.2k • written 17 months ago by ▴ 30
0
votes
1
reply
1.5k
views
Comment: Comment: Which threshold to be put in the MAPQ when doing mpileup of BCF tools on a STAR-
17 months ago by mohsamir2016 ▴ 30
0
votes
0
replies
1.5k
views
Comment: Comment: Which threshold to be put in the MAPQ when doing mpileup of BCF tools on a STAR-
17 months ago by mohsamir2016 ▴ 30
0
votes
0
replies
1.9k
views
Comment: Comment: Number of PCR duplicates in STAR-generated BAM file have no duplicate before and
17 months ago by mohsamir2016 ▴ 30
3
votes
8
replies
1.9k
views
Number of PCR duplicates in STAR-generated BAM file have no duplicate before and after fixmate/duplicate removal ?
RNA-seq STAR
updated 14 months ago by 43k • written 17 months ago by ▴ 30
0
votes
0
replies
1.9k
views
Comment: Comment: Number of PCR duplicates in STAR-generated BAM file have no duplicate before and
17 months ago by mohsamir2016 ▴ 30
0
votes
1
reply
1.9k
views
Comment: Comment: Number of PCR duplicates in STAR-generated BAM file have no duplicate before and
17 months ago by mohsamir2016 ▴ 30
0
votes
0
replies
1.9k
views
Comment: Comment: Number of PCR duplicates in STAR-generated BAM file have no duplicate before and
17 months ago by mohsamir2016 ▴ 30
1
vote
12
replies
3.1k
views
Confused about % of mapped and unmapped reads output from STAR aligner
RNAseq STAR
updated 7 months ago by 43k • written 18 months ago by ▴ 30
0
votes
0
replies
3.1k
views
Comment: Comment: Confused about % of mapped and unmapped reads output from STAR aligner
17 months ago by mohsamir2016 ▴ 30
0
votes
1
reply
3.1k
views
Comment: Comment: Confused about % of mapped and unmapped reads output from STAR aligner
updated 17 months ago by 43k • written 17 months ago by ▴ 30
0
votes
0
replies
326
views
Better understanding of STAR statistical summary
RNA-seq STAR
updated 14 months ago by 43k • written 18 months ago by ▴ 30
0
votes
1
reply
3.1k
views
Comment: Comment: Confused about % of mapped and unmapped reads output from STAR aligner
18 months ago by mohsamir2016 ▴ 30
0
votes
1
reply
3.1k
views
Comment: Comment: Confused about % of mapped and unmapped reads output from STAR aligner
18 months ago by mohsamir2016 ▴ 30
0
votes
2
replies
3.1k
views
Comment: Comment: Confused about % of mapped and unmapped reads output from STAR aligner
18 months ago by mohsamir2016 ▴ 30
3
votes
7
replies
2.3k
views
Confused with output of STAR aligner for paired end reads and need advice on closely related SNPs analyses
RNA-seq
updated 14 months ago by 43k • written 18 months ago by ▴ 30
0
votes
2
replies
2.3k
views
Comment: Comment: Confused with output of STAR aligner for paired end reads and need advice on clo
updated 14 months ago by 43k • written 18 months ago by ▴ 30
0
votes
0
replies
2.3k
views
Comment: Comment: Confused with output of STAR aligner for paired end reads and need advice on clo
18 months ago by mohsamir2016 ▴ 30
0
votes
1
reply
2.3k
views
Comment: Comment: Confused with output of STAR aligner for paired end reads and need advice on clo
updated 14 months ago by 43k • written 18 months ago by ▴ 30
0
votes
1
reply
767
views
How can I descending reorder the dots in the scatter plot in ggplot based on the X values ?
RNA seq
updated 19 months ago by ★ 1.8k • written 19 months ago by ▴ 30
4
votes
3
replies
708
views
Confused about which comparison to give a more accurate answer in RNA seq experimen t
RNA seq
updated 19 months ago by 14k • written 19 months ago by ▴ 30
0
votes
1
reply
708
views
Comment: Comment: Confused about which comparison to give a more accurate answer in RNA seq experi
19 months ago by mohsamir2016 ▴ 30
0
votes
0
replies
284
views
Should the least DE genes are the same as the ones with least tagwise dispersion in EdgeR ?
RNA seq
19 months ago by mohsamir2016 ▴ 30
0
votes
0
replies
345
views
Should the least DE genes are the same as the ones with least tagwise dispersion in EdgeR ?
edgeR RNA-seq
updated 21 months ago by 82k • written 21 months ago by ▴ 30
0
votes
2
replies
583
views
Plotting multiple genes across 4- species
RNA seq
updated 21 months ago by 14k • written 21 months ago by ▴ 30
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