Hi I am fairly new to RNA-seq.
I am trying to analyze my data using segemehl but am running into following error. (I've cut and pasted the last part of the output.)
[SEGEMEHL] Fri Jul 24 19:16:53 2015: 1637977 reads in thread 0.
[SEGEMEHL] Fri Jul 24 19:16:53 2015: 1637824 reads in thread 1.
[SEGEMEHL] Fri Jul 24 19:16:53 2015: 1637824 reads in thread 2.
[SEGEMEHL] Fri Jul 24 19:16:53 2015: 1637824 reads in thread 3.
segemehl.x: libs/biofiles.c:1160: bl_fastxAddMate: Assertion `bl_fastaCheckMateID(f, n, descr, descrlen)' failed.
My job commend is
segemehl.x --silent -i hg19.idx -d human_hg19.fa -q READ1 -p READ2 -O -o sege.sam -u unmap.sam -D 1 -t 4
One of my question was if I submit the job by chromosome to reduce the memory load how can segemehl map reads that align to different chromosomes?
I read in some posting I should use the full reference file for but this will lead to significant increase in mapping time and memory requirement.
How do I find the right balance?
Thank you in advance
I am trying to analyze my data using segemehl but am running into following error. (I've cut and pasted the last part of the output.)
[SEGEMEHL] Fri Jul 24 19:16:53 2015: 1637977 reads in thread 0.
[SEGEMEHL] Fri Jul 24 19:16:53 2015: 1637824 reads in thread 1.
[SEGEMEHL] Fri Jul 24 19:16:53 2015: 1637824 reads in thread 2.
[SEGEMEHL] Fri Jul 24 19:16:53 2015: 1637824 reads in thread 3.
segemehl.x: libs/biofiles.c:1160: bl_fastxAddMate: Assertion `bl_fastaCheckMateID(f, n, descr, descrlen)' failed.
My job commend is
segemehl.x --silent -i hg19.idx -d human_hg19.fa -q READ1 -p READ2 -O -o sege.sam -u unmap.sam -D 1 -t 4
One of my question was if I submit the job by chromosome to reduce the memory load how can segemehl map reads that align to different chromosomes?
I read in some posting I should use the full reference file for but this will lead to significant increase in mapping time and memory requirement.
How do I find the right balance?
Thank you in advance
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