Question: SRA to FASTQ problem
0
gravatar for m.t.lorenc
21 months ago by
m.t.lorenc0
m.t.lorenc0 wrote:

Hi, I downloaded RNA-Seq data from NCBI and used fastq-dump --gzip --skip-technical --readids --read-filter pass --dumpbase --split-3 --clip SRR1043177.sra to convert into FASTQ. However, it appears that header in @ and + are different:

> zcat SRR1043177_pass_1.fastq.gz | head
@HWI-ST960:133:C1FJJACXX:6:1101:1708:2209/1
TNAAACTTAAAGGAAAAACATGGAATTTGTTTCTATGTTCTGCTTATTTGCGATTGTTTCTTTCTCTCTTCNNNNNNNNNATTCNNNNTNCNNNNTCNTG
+SRR1043177.1.1 HWI-ST960:133:C1FJJACXX:6:1101:1708:2209 length=100
@#1=DDFFHHHHGIIJIJIJJHIIFIIJJCGIJJJJJIIDDGGHIJGIIJFHFBGHFHHFHGIGIGHGJJC#############################

This caused an error in trim_galore

trim_galore -o /scratch/waterhouse_team/tmp/galore --cores 2 --paired NbSRR_WtR1.fastq.gz NbSRR_WtR2.fastq.gz
...
cutadapt: error: Error in FASTQ file at line 3: Sequence descriptions don't match ('HWI-ST960:133:C1FJJACXX:6:1101:1708:2209/1' != 'SRR1043177.1.1 HWI-ST960:133:C1FJJACXX:6:1101:1708:2209 length=100').
The second sequence description must be either empty or equal to the first description.

How it possible to fix the FASTQ file?

Thank you in advance,

sequencing rna-seq next-gen • 799 views
ADD COMMENTlink modified 21 months ago by ATpoint46k • written 21 months ago by m.t.lorenc0
3
gravatar for ATpoint
21 months ago by
ATpoint46k
ATpoint46k wrote:

You need to pass option --origfmt to fastq-dump to make it not append /1 to forward reads and /2 to reverse reads. Rather than that it will use the original read names from the sequencer so that the two read names are fully identical.

ADD COMMENTlink written 21 months ago by ATpoint46k
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