User Timur Shtatland - Bioinformatics Stack Exchange

7 votes

Accepted

How is the GT field in a VCF file defined?

answered Sep 14, 2020 at 12:13

5 votes

Accepted

Telling grep to treat N as [ATCG]

answered Mar 24, 2021 at 1:39

5 votes

Cannot obtain alignment summary after running Bowtie2

answered Oct 18, 2023 at 21:09

4 votes

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How can I export a full alignment from IGV as an image?

answered Nov 4, 2019 at 16:44

4 votes

Accepted

Edit all the fasta headers using awk

answered Feb 12, 2020 at 17:27

3 votes

Method to detect genome doubling

answered Nov 8, 2019 at 2:53

3 votes

Error with BWA Mem input having multiple fastq files using cat and process substitution

answered Nov 8, 2019 at 14:55

3 votes

How I can change the name of multiple files at once in R or terminal?

answered Nov 9, 2019 at 22:30

3 votes

Filtering columns from large file based on a column list

answered Nov 7, 2023 at 18:53

3 votes

Accepted

Using python to call Emboss wordcount

answered Oct 30, 2021 at 0:59

2 votes

Accepted

Bedtools get fasta and ORF from a blastX run

answered Nov 14, 2019 at 12:55

2 votes

Produce .vcf file of ALL mutations in .bam file

answered Aug 12, 2020 at 20:18

2 votes

Accepted

How can I extract information from .sam files?

answered Jan 26, 2021 at 20:04

2 votes

How to get rows with similar values in two different columns using command line?

answered Oct 3, 2020 at 15:41

1 vote

BLASTn query coverage discrepancy

answered Oct 4, 2020 at 16:59

1 vote

Accepted

How to get matching pattern along with ID in a single command in grep?

answered Jan 17, 2021 at 21:40

1 vote

Accepted

Mapping statistics from bam file using bbtools and sambamba

answered Sep 27, 2020 at 13:55

1 vote

Quantify low complexity regions in DNA sequences

answered Mar 1, 2021 at 18:37

1 vote

How to copy only certain counts for genes in tsv file to new file in linux

answered Sep 26, 2021 at 21:24

1 vote

How to measure the total size of a fastq file in base pairs?

answered Sep 1, 2020 at 13:11

1 vote

how to calculate coverage of each base of mapped reads?

answered Jan 27, 2020 at 17:39

1 vote

How do I find unique file names without their extensions in shell script?

answered Jun 3, 2022 at 17:43

0 votes

Filter bam with sambamba

answered Jun 6, 2022 at 15:00

0 votes

Accepted

DNA seq cutting using Linux

answered Aug 8, 2020 at 20:32

Stack Exchange Network

24 Answers

How is the GT field in a VCF file defined?

Telling grep to treat N as [ATCG]

Cannot obtain alignment summary after running Bowtie2

How can I export a full alignment from IGV as an image?

Edit all the fasta headers using awk

Method to detect genome doubling

Error with BWA Mem input having multiple fastq files using cat and process substitution

How I can change the name of multiple files at once in R or terminal?

Filtering columns from large file based on a column list

Using python to call Emboss wordcount

Bedtools get fasta and ORF from a blastX run

Produce .vcf file of ALL mutations in .bam file

How can I extract information from .sam files?

How to get rows with similar values in two different columns using command line?

BLASTn query coverage discrepancy

How to get matching pattern along with ID in a single command in grep?

Mapping statistics from bam file using bbtools and sambamba

Quantify low complexity regions in DNA sequences

How to copy only certain counts for genes in tsv file to new file in linux

How to measure the total size of a fastq file in base pairs?

how to calculate coverage of each base of mapped reads?

How do I find unique file names without their extensions in shell script?

Filter bam with sambamba

DNA seq cutting using Linux