search

FelixKrueger / TrimGalore

A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data
GNU General Public License v3.0
461 stars 150 forks source link

TrimGalored sequence cannot be mapped with Bowtie2 #135

Closed moqri closed 1 year ago

moqri commented 2 years ago

When I use TrimGalore, some of my trimmed files cannot be mapped using Bowtie2.

Example: SRR11908644 raw data trimmed using TrimGalore then fed into Bowtie2 results in:

Saw ASCII character 10 but expected 33-based Phred qual.
terminate called after throwing an instance of 'int'
Saw ASCII character (ERR): bowtie2-align died with signal 6 (ABRT)

Any suggestions?

FelixKrueger commented 2 years ago

This is very strange, but I doubt it has anything to do with Trim Galore to be honest. Can you run FastQC on the file without any issues?

FelixKrueger commented 1 year ago

Haven't heard back in a long time.