batch renaming FASTQ files

Question

[amitpande74]

Hi,

I have 40 fastq files named as

SRR1313062_GSM1401648_ZR-75-1_Homo_sapiens_RNA-Seq_1.fastq.gz  
SRR1313062_GSM1401648_ZR-75-1_Homo_sapiens_RNA-Seq_2.fastq.gz

until

SRR1313131_GSM1401717_06-01-A009b_Homo_sapiens_RNA-Seq_1.fastq.gz
SRR1313131_GSM1401717_06-01-A009b_Homo_sapiens_RNA-Seq_2.fastq.gz

I want to change these names to

SRR1313062_1.fastq.gz  
SRR1313062_2.fastq.gz

and so on until

SRR1313131_1.fastq.gz 
SRR1313131_2.fastq.gz

Have tried :

rename  's/(\w_).*_(R[0-9])_.*(.fastq.gz)/$1$2$3/' filenames

and

brename -p '^(\w+)_.+_.+(_R[12]_).+' -r '${1}$2.fastq.gz' filenames

but nothing is working. Can someone kindly help.

[cpad0112]

If _GSM...RNA-seq is common in all names, keep it simple:

$ rename -n  's/_GSM.*_RNA-Seq//' *.gz

with parallel

parallel --dry-run mv {} /new_folder/{=s/_GSM.\*_RNA-Seq//=} ::: *.gz

If you would like to use regex, use following:

$ rename -n  's/^(.*)_GSM.*(_[12])/$1$2/' *.gz

[shenwei356]

The brename version should be

brename -p '^(\w+?)_.+([12]).fastq.gz$' -r '${1}_$2.fastq.gz'

Answer 1

[tshtatland]

Use rename:

Dry run:

rename -n 's{ ^ ( [^_]* ) .* ( _[12].fastq.gz ) $ }{$1$2}x' *.fastq.gz

Actually rename:

rename 's{ ^ ( [^_]* ) .* ( _[12].fastq.gz ) $ }{$1$2}x' *.fastq.gz

The command-line utility rename comes in many flavors. Most of them should work for this task. I used the rename version 1.601 by Aristotle Pagaltzis. To install rename, simply download its Perl script and place it into $PATH. Or install rename using conda, like so:

conda install rename

Answer 2

[jonathnjohn77]

you can do with with catenation command also

cat SRR1313062_GSM1401648_ZR-75-1_Homo_sapiens_RNA-Seq_1.fastq.gz > SRR1313062_1.fastq.gz

[Friederike]

Some reasons why I wouldn't go with this proposal:

• if you're dealing with a gz file, zcat would be more appropriate;
• the solution presented here would also create copies of every single file;
• plus it does not address the original issue, which had to do with performing the task in batch