Question: Problem in TRim Galore
0
majeedaasim • 50 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?
ADD COMMENT
• link
•
modified 3.1 years ago
by
GenoMax ♦ 95k
•
written
3.1 years ago by
majeedaasim • 50
Get the fastq reads directly from EBI-ENA for SRX485643 avoiding these types of issues with SRA.
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.