[khmer] khmer stripped header information from RNA-seq reads, rendering them unusable

Erich Marquard Schwarz ems394 at cornell.edu
Thu Jul 17 11:12:02 PDT 2014


On Jul 17, 2014, at 2:00 PM, Philipp Schiffer <philipp.schiffer at gmail.com> wrote:

> I guess this [stripping of information from newer-Illumina-style FastQ header lines] is supposed to happen...

    For some value of "supposed", but it is not optimal.  If it could be corrected in a future version of khmer, that would be good indeed!

    I am running a Perl script to retrofit the FastQ headers with '#0/1' and '#0/2' (which was Illumina's older style of distinguishing paired-end reads).


--Erich





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