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Forum: Bioinformatics 11-30-2013, 04:22 PM
Replies: 2
Views: 2,837
Posted By arm55
norafar, include the - file marker as output on...

norafar, include the - file marker as output on the sort and it should work.

samtools sort -on -m 300000000 accepted_hits.bam - | samtools view -h - | htseq-count -m union - hg19.gtf > output.count
Forum: Bioinformatics 11-30-2013, 03:52 PM
Replies: 2
Views: 1,856
Posted By arm55
You seem to be confusing coverage and read...

You seem to be confusing coverage and read length. Coverage is the depth of the sequencing, or the average number of reads covering any particular nucleotide.

When you go from 2x100 to 2x150,...
Forum: Bioinformatics 02-06-2013, 12:22 PM
Replies: 16
Views: 3,984
Posted By arm55
Hi Joe, If your file is missing the @SQ...

Hi Joe,

If your file is missing the @SQ header lines, you will need your reference file, *.fa, in order to convert to BAM. The command will look like:


Let me know if that works.

Cheers,
...
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