FASTQ header correction to remove .1 and .2 from paired end - SRA files
From this step as raw data:
@ERR797585640.1.1 1 length=151
ATATCGGGACGTGCGATCAGCACAAGCCGGCTATCGGTGTGGCGC
I have converted till this:
Read 1:
@ERR797585640.1.1
ATATCGGGACGTGCGATCAGCACAAGCCGGCTATCGGTGT
Read 2:
@ERR797585640.1.2
ATATCGGGACGTGCGATCAGCACAAGCCGGCTATCGGTGT
I have taken ERR and SRA samples for RnD.
But I want to keep only format as:
Read 1:
@ERR797585640.1
ATATCGGGACGTGCGATCAGCACAAGCCGGCTATCGGTGT
Read 2:
@ERR797585640.1
ATATCGGGACGTGCGATCAGCACAAGCCGGCTATCGGTGT
Kindly provide any commands or suggestion to remove and make changes for fastq headers
• 1,539 views
•
link
updated
by
noodle
•
written
by
genomics_buddy •
•
written
by
genomics_buddy •
1 answer
Not sure it's a good idea to name both reads the same, but here's a perl oneliner to change your FASTQ headers:
perl -lne 'if(/^(@[^\.)]+\.\d+)\.\d/){ print "$1" } else { print }'
If you want to make sure only headers are affected, in case quality line starts with at:
perl -lne 'if($.%4==1 && /^(@[^\.)]+\.\d+)\.\d/){ print "$1" } else { print }'
• 0 views
•
link
written
by
b.contreras.moreira •
Log in to answer this question.
More posts like this
-
Tutorial: GEO data mining (IB) - Downloading Sequence Read Archive (SRA) raw data
written by Novogene •
-
Rna Seq Analysis Script
written by SomeOne •
-
ATAC seq - Estimated fragment size from MACS2 and Homer
written by emalekos •
-
Troubleshooting Missing_Read_Group and Mismatch_Flag_Mate Errors
written by shpak.max •
-
fastq headers problem with Trinity
written by agata •
-
Assembly finished but output contig file is empty
written by tchow5 •
-
GWAS imputation and quality control
written by a95087a8d7 •
-
Question about cd-hit-otu's parameter
written by qhsh9713 •
-
Trimmomatic adapter.fa file with gene name, forward primer and reverse primer
written by m.ghanatbari •
-
Error reading nexus(.nex) file in R
written by Mani •
how ? what was the command ?
I have used:
But i need further guidance for next step
you cannot use '@' as the signal for the first line of a fastq file as @ can also be a symbol of quality
Please stop using "convert", you're using it wrong and your sentences don't make any sense.