I'm using SpliceMap to align my short read data (fastq files with 36 bp pair-end reads). Since it appears that SpliceMap requires reads of length 50 after clipping, all of the reads are being excluded. Does anyone know a way around this?
I thought about modifying the source code to be fine with reads 36 bp long but it's tricky for me since the the files (e.g. runSpliceMap) don't open as human readable code.
I'm using version 3.3.5.2 of SpliceMap.
A snippet of the screen output:
I'd like to use SpliceMap because it's recommended by IDP-fusion (which is the next step in my analysis) for producing the alignment sam and junction detection bed files.
I thought about modifying the source code to be fine with reads 36 bp long but it's tricky for me since the the files (e.g. runSpliceMap) don't open as human readable code.
I'm using version 3.3.5.2 of SpliceMap.
A snippet of the screen output:
Preparing the reads!...
Bases removed from front: 0
Using as many bases as possible.
Warning: excluding line temp/read_1_1|2(less than 50bp after clipping)
Warning: excluding line temp/read_1_2|2(less than 50bp after clipping)
Warning: excluding line temp/read_1_1|6(less than 50bp after clipping)
Warning: excluding line temp/read_1_2|6(less than 50bp after clipping)
Warning: excluding line temp/read_1_1|10(less than 50bp after clipping)
Warning: excluding line temp/read_1_2|10(less than 50bp after clipping)
Warning: excluding line temp/read_1_1|14(less than 50bp after clipping)
Warning: excluding line temp/read_1_2|14(less than 50bp after clipping)
Bases removed from front: 0
Using as many bases as possible.
Warning: excluding line temp/read_1_1|2(less than 50bp after clipping)
Warning: excluding line temp/read_1_2|2(less than 50bp after clipping)
Warning: excluding line temp/read_1_1|6(less than 50bp after clipping)
Warning: excluding line temp/read_1_2|6(less than 50bp after clipping)
Warning: excluding line temp/read_1_1|10(less than 50bp after clipping)
Warning: excluding line temp/read_1_2|10(less than 50bp after clipping)
Warning: excluding line temp/read_1_1|14(less than 50bp after clipping)
Warning: excluding line temp/read_1_2|14(less than 50bp after clipping)
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