User: mg

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mg20
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Posts by mg

<prev • 4 results • page 1 of 1 • next >
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Answer: A: Sequence length from Fasta
... Using [SeqKit's fx2tab](https://bioinf.shenwei.me/seqkit/usage/#fx2tab-tab2fx): ``` seqkit fx2tab --length --name --header-line foo.fasta ``` This prints sequence name and length with empty columns for sequences and qualities. ...
written 5 weeks ago by mg20
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Answer: A: How to extract specific chromosome from vcf file
... [bcftools](http://samtools.github.io/bcftools/bcftools-man.html#view) can be used, and this will preserve the header as well. bcftools view input.vcf.gz --regions chr1 To extract mutiple chromosomes pass them as comma separated. eg. `--regions chr1,chr5` ...
written 7 months ago by mg20
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Identifying coverage differences in two WGS platforms
... I am comparing data from two whole genome sequencing platforms and would like to find out if one platform covers certain regions better than others (and why)? Would you recommend any tool(s) to do such comparison? Also, one platform used hg19 as reference sequence as reference genome, whereas the ...
genome next-gen sequencing written 8 months ago by mg20 • updated 8 months ago by ATpoint9.5k
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Comment: C: How To Split A Bam File By Chromosome
... Is it possible to specify output directory, and to mention which specify chromosome needs to be extracted (for eg., just chr5 and chr22)? ...
written 9 months ago by mg20

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