trimming paired end reads using Trim galore

[Hedi86]

Dear all

im trying to trim paired-end RRBS illumina reads using Trim galore. as far as i understood, paired end reads must be trimmed using --paired option following by file names. i tried : trim_galore --paired r1.fastq.gz r2.fastq.gz. however at the end, im getting only trimmed file for read 1 and nothing for read 2. any idea why?

thank you so much in advance

[fkrueger]

Hi Hedi86,

for RRBS the command would be:

trim_galore --rrbs --paired r1.fastq.gz r2.fastq.gz

Which version of Trim Galore were you using (the latest one is v0.5.0, https://github.com/FelixKrueger/TrimGalore/releases).

Trim Galore will trim R1 first, R2 second, and then perform a validation step which p0roduces 2 new files that contain _val_ in their file names (for validated). Once this is done, the files called _trimmed_ ... are being deleted. If there are any error messages on the screen they might help identify where the problem lies.

[Hedi86]

thank you for your replay

for downstream analyses in Bismark i used both Val-trimmed-R1 and Val-trimmed-R2 files (because libraries prepared using NuGEN kit). however, bismark produced only one BAM file with R1 extension name. is it normal for pair end alignment?

Best

[fkrueger]

Yes, this is normal. Paired-end BAM files have Read 1 and Read 2 on consecutive lines, so there is only one file per read pair.

[ashishbansal]

These are steps to work on trimming process.

Step 1: Quality*Trimming. In the first step, low-quality base calls are*trimmedoff from the 3'*end*of the*reads*before adapter removal.
Step 2: Adapter*Trimming.
Step 3: Removing Short Sequences.
Step 4: Specialised*Trimming.