cutadapt cannot work on my fastq files
Hi,
I download .sra files from NCBI and convert them into fastq file by fastq-dump. So when I try to use cutadapt to trim my data, it shows:
cutadapt -a AGATCGGAAGAGC -o SRR1658373.trimmed.fastq SRR1658373.fastq >> trim_report.txt
Error: at line 1, expected a line starting with '+'
So I head my fastq file, it shows:
Read 47403478 spots for SRR1658373.sra
Written 47403478 spots for SRR1658373.sra
ATGCAAATGCTTCTCAGATGATGAAAACTATTAGTATAACTGCTGTTAGGGAAATGAATGAGCCTATTGATGAGATAGTATTTCA
+SRR1658373.1 HWI-ST538:365:C2NBHACXX:1:1101:7347:2000 length=100
;7;###4<@@@@@@@@@@???@@@@@@??@?@@?@???????????????????????@@@@@@@@@@@@@??@@?@@@@@@???????????=>?????
@SRR1658373.2 HWI-ST538:365:C2NBHACXX:1:1101:1485:2103 length=100
CCAATAAAGATGGCCTAAGGTGACCTTCAACCAGAAATCCCCATGTCAGTGACACGTAAAACATGACAGCACCTTCAACACAACATGCAACCCAGACCCA
+SRR1658373.2 HWI-ST538:365:C2NBHACXX:1:1101:1485:2103 length=100
CCCFFFFFHHDHFHIGHIGIAEFHJIJIIJJIIJJJJGIIJJJJJIIJIHIFHIIIHGJIJIGHGIJJIIHHGHH@D>DFDDDDDDDDDDDDDDDBDDDD
How to make the fastq file capable for cutadapt? How to edit first 2 lines of fastq file?
Thanks a lot for the help!
Best,
Ellie
1 answer
while running fastq-dump, you don't need to redirect the output. remove the > from your command. Just run
fastq-dump SRR1658373.sra
Read the documentation once and use appropriate options for your data.
• 0 views
•
link
updated
by
Ram
•
written
by
GouthamAtla
•
written
by
GouthamAtla
Log in to answer this question.
More posts like this
Are these a part of your fastq files ? can you show the fastq-dump command ?
Thanks for the quick answer, here is my command for download files from NCBI:
Then I upload SRR1658373 to a server, then did the fastq-dump by using:
Will the different version of sratoolkit causes this problem?