User: johnston.mike.j

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Posts by johnston.mike.j

<prev • 4 results • page 1 of 1 • next >
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Answer: A: Writing vcf file headers
... It seems that the contig header lines are incorrect. If you have access to the genome fasta index that was used for the analysis, the following script should remove the existing '##contig' lines and replace them with the correct details from the fasta index. # Input / output filenames index ...
written 13 days ago by johnston.mike.j10
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Answer: A: Subsampling with BBtools by read number
... The `reformat.sh` option `samplereadstarget` seems to be exactly what you want. To subsample 1M reads from a file, I ran: reformat.sh \ in=input.fq \ out=output.fq \ samplereadstarget=1000000 \ sampleseed=13 To check: wc -l output.fq 4000000 -- as expecte ...
written 10 weeks ago by johnston.mike.j10
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Comment: C: How to count the total aligned bases in BAM?
... I am worried that this will significantly underestimate the number of aligned bases. With -bga, each row has one coverage value for *a range of bases*, not *each individual base*. Illustrated in the manual here: [https://bedtools.readthedocs.io/en/latest/content/tools/genomecov.html][1] You would n ...
written 9 months ago by johnston.mike.j10
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Comment: C: Kallisto pseudobam to IGV
... The gencode annotation was the issue for me as well. The following command edits the gencode fasta read headers to only include the first transcript field: sed -r 's/^(>[^\|]+)\|.*/\1/g' gencode.v28.transcripts.fa > gencode.v28.transcripts.onlyTxLineHeaders.fa After reindexing on this f ...
written 2.1 years ago by johnston.mike.j10

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