Tweet
Hi,
My RNA-seq data has transcript fusions and novel splice-junctions. So, I am trying to use segemehl in local alignment (-S) mode to map it. I am using the -Z 20 (--minfraglen <n> min length of a spliced fragment). However, I get fragments of length <20 nt in my output. The command for mapping looks like this-
~/bin/segemehl/segemehl.x --silent -d reference.fa -q reads.fastq -i reference.idx -o file.sam -S -A 95 -Z 20
Example output,
M02096:114:000000000-AEH6V:1:1106:27332:13940 1:N:0:1 16 XIST 78 255 9M * 0 0 TTTCTCTTG IIIFIIIII NM:i:0 MD:Z:9 NH:i:1 XI:i:0 XL:i:2 XA:Z:Q XX:i:223 XY:i:231 XQ:i:1 XP:Z:XIST XU:i:990 XS:i:0
Can someone please explain if I am doing something wrong? Why do I see alignments of <20 nt even after specifying -Z 20?
My RNA-seq data has transcript fusions and novel splice-junctions. So, I am trying to use segemehl in local alignment (-S) mode to map it. I am using the -Z 20 (--minfraglen <n> min length of a spliced fragment). However, I get fragments of length <20 nt in my output. The command for mapping looks like this-
~/bin/segemehl/segemehl.x --silent -d reference.fa -q reads.fastq -i reference.idx -o file.sam -S -A 95 -Z 20
Example output,
M02096:114:000000000-AEH6V:1:1106:27332:13940 1:N:0:1 16 XIST 78 255 9M * 0 0 TTTCTCTTG IIIFIIIII NM:i:0 MD:Z:9 NH:i:1 XI:i:0 XL:i:2 XA:Z:Q XX:i:223 XY:i:231 XQ:i:1 XP:Z:XIST XU:i:990 XS:i:0
Can someone please explain if I am doing something wrong? Why do I see alignments of <20 nt even after specifying -Z 20?