TopHat: SE reads

[maria_mari]

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

[AnotherHTS]

have you tried decreasing the --segment-length ?

Tophat splits your reads up into smaller segments (25bp by default), which it tries to align individually. If your reads are short, you may need to manually specify a smaller segment size.

[maria_mari]

have you tried decreasing the --segment-length ?

Tophat splits your reads up into smaller segments (25bp by default), which it tries to align individually. If your reads are short, you may need to manually specify a smaller segment size.

my read length=28, if I choose 14, isn't it too short?

[Dario1984]

Why is it 28 ? What is your protocol ? It would be a bit too short for most programs to do spliced alignments for it.

[AnotherHTS]

my read length=28, if I choose 14, isn't it too short?

I am not sure if there is minimum value on --segment-length.

If you still have problems perhaps you can get around it by disabling the coverage search feature with "--no-coverage-search".