SpliceMap: all reads less than 50bp after clipping

[belgravia]

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:

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)

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.

[g3n3]

I'm Jason, Postdoc in Kin Fai's lab familiar with IDP. Thanks for your question and linking the SeqAnswers post. I'll post up the same response there.

IDP was written with fairly rigid input requirements but we have several scripts to help open up more options for valid inputs to IDP. We have scripts that allow us to substitute hisat aligned short reads for the splicemap aligned short reads.

To get the necessary scripts, you can clone our lab's public repository:
$ git clone https://github.com/jason-weirather/Au-public.git

And then add
Au-public/iron/pythonlib/

to your python path, i.e.:
edit ~/.bashrc and add the line
export PYTHONPATH=$PYTHONPATH:<path to source>/Au-public/iron/pythonlib

The utilities I refer to are found in
Au-public/iron/utilities/

IDP requires a short read alignment as well as junctions
of known splices and to add on splices for predicted isoforms and to
do the quantification.

We have a script to make the output of hisat alignment compatible with IDP (not yet compatible with
hisat2, sorry). After hisat alignment you can convert the output sam/bam into a
splicemap-like sam and a corresponding junction bed file.

make_sam_splicemap_like.py

https://github.com/jason-weirather/Au-public/blob/master/iron/utilities/make_sam_splicemap_like.py

sam_to_splicemap_junction_bed.py

https://github.com/jason-weirather/Au-public/blob/master/iron/utilities/sam_to_splicemap_junction_bed.py

Are the two scripts that can accomplish this. If you have trouble running these please let me know.

Thanks!