Tophat: Se Reads

Question

[RandManP]

Hi All, Can anybody help me how to run tophat for SE data?

I ran the following command but I got an warning and error

tophat --bowtie1 -p 4 -G mouse.gtf -o a_thout mouse/mouse_index/mouse a.fastq

Warning: you have only one segment per read.
If the read length is greater than or equal to 45bp,
we strongly recommend that you decrease --segment-length to about half the read length because TopHat will work better with multiple segments

Mapping left_kept_reads.m2g_um against mouse with Bowtie
[FAILED]
Error: segment-based junction search failed with err =127

Thank you

Answer 1

[Pavel Senin]

(1) I would try to run without -p 4, i.e. using a single thread (2) I would configure the segment length so it could infer splice sites/junctions