0
0
Entering edit mode
4.6 years ago
woongjaej ▴ 20

Hi, guys.

I'm having trouble using cutadapt to trim the raw read(single-end) of small RNA seq.(Illumina TruSeq) I got the index information of the adapter from the sequencing facility. So I tried to trim adapters using cutadapt like below

cutadapt -b TGGAATTCTCGGGTGCCAAGG -b AACTCCAGTCAC"$INDEX_SEQ"ATCTCGTATGCC -O 3 -m 17 -o$trimmed_fastq.gz $fastq.gz The first adapter is Illumina Samll RNA Adapter and the second one is the adapter information including index(bold 6 bases). But the fastqc report of trimmed read gives me there's TGGAATTCTCGGGTGCCAAGG sequence still over represented~!. So if I go cutadapt again "-b TGGAATTCTCGGGTGCCAAGG" for$trimmed_fastq.gz, then they are gone. Why doesn't cutadapt get rid of TGGAATTCTCGGGTGCCAAGG at the first time?

Thank you

cutadapt smRNA-seq trimming Illumina • 3.2k views
0
Entering edit mode

You should be able to see in the log file how many times it found each adapter in each position. Try to compare the two runs.

0
Entering edit mode

I tried to compare the tow runs. First trimming result tells me it trimmed for 13298819 items for the first adapter. And then second trimming tells me it trimmed for 432477 items. Doesn't this mean cutadapt failed to trim for all of the "TGGAATTCTCGGGTGCCAAGG" adapter sequences??

0
Entering edit mode

Looks like it. That's weird.

0
Entering edit mode

Nothing to say in that case.

Putting bbduk.sh from BBMap out there in case you are able to use a different program. Option to use would be literal=TGGAATTCTCGGGTGCCAAGG,AACTCCAGTCAC

0
Entering edit mode

Thank you genomax!

I'll try to compare results from the both. Thank you for your advice