Comments (6)
right! i only ever tested with 1 & 2.... i will fix today. thanks
Original comment by [email protected]
on 2 Oct 2013 at 3:35
from ea-utils.
Thanks for looking into this! And for the terrific tool
(fast/efficient/flexible with pipeable output)
Do use the attached files instead. The ones above have no Ns post filtering in
test1
Also, I should have said, I tried all combinations of one or both of: --max-ns
0 and --mate-max-ns 0, but got the same results in all cases:
fastq-mcf --max-ns 0 --mate-max-ns 0 -o test1 -o test2 -R adapters.fa
test1.fq.gz test2.fq.gz
awk '(NR+2)%4==0' test1 | grep -c N
4
awk '(NR+2)%4==0' test2 | grep -c N
41
----
as you said --max-ns or --mate-max-ns 1 or 2 seem to work fine.
Original comment by [email protected]
on 2 Oct 2013 at 4:04
Attachments:
from ea-utils.
I just tried changing line number 1286 in fastq-mcf.c (in
ea-utils.1.1.2-537.tar.gz) to:
if (t_max_ns >= 0) {
and it seemed to do the trick.
Original comment by [email protected]
on 3 Oct 2013 at 1:08
from ea-utils.
yep, that's the same change i just made (and checked in)
Original comment by [email protected]
on 3 Oct 2013 at 1:09
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Thanks so much!
Original comment by [email protected]
on 3 Oct 2013 at 1:10
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Original comment by [email protected]
on 3 Oct 2013 at 1:51
- Changed state: Fixed
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