Question: Problem in TRim Galore
0
gravatar for majeedaasim
21 months ago by
majeedaasim40
United States
majeedaasim40 wrote:

I have down loaded the SRA file from using fast-dump

as

fastq-dump  -A SRX485643 --skip-technical  --readids --dumpbase --split-3 --clip SRR_ID

It produced 2 files 1 and 2 when I ran TRim Galore on it as

trim_galore --phred64 --fastqc Ephedra_sinica_left.fastq Ephedra_sinica_right.fastq

Following error message is shown

This is cutadapt 1.15 with Python 3.6.2
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC Ephedra_sinica_left.fastq
Running on 1 core
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
cutadapt: error: At line 3: Sequence descriptions in the FASTQ file don't match ('HWI-ST915_0064:2:1101:1420:2104/1' != 'SRR1188607.1 HWI-ST915_0064:2:1101:1420:2104 length=100').
The second sequence description must be either empty or equal to the first description.

How can I modify the description to match each other?

trim galore eror • 749 views
ADD COMMENTlink modified 21 months ago by genomax72k • written 21 months ago by majeedaasim40
1

Get the fastq reads directly from EBI-ENA for SRX485643 avoiding these types of issues with SRA.

ADD REPLYlink written 21 months ago by genomax72k

I never used TrimGalore, but the error message ( Trimming 1 adapter with at most 10.0% errors in single-end mode ... ) suggests it is expecting single-end fastq files, not paired end.

ADD REPLYlink written 21 months ago by h.mon27k
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