Extract sequences from a FASTQ file based on another file

caputcastellae · 08-14-2014, 12:39 PM

I have two files:

file 1: fastaq XXGB file
file 2: list of a few FASTQ ID headers formatted as follows:

@M01032:192:000000000-AAEFT:1:1101:10100:1004 2:N:0:1
@M01032:192:000000000-AAEFT:1:1101:10100:1004 1:N:0:1

Is there an easy way (perl?) to generate a third file with the info (including the ID headers of the targeted sequences (file 2)?

Thanks!

GenoMax · 08-14-2014, 01:03 PM

There are probably more elegant ways of doing this but you can try this now. With that said (in tcshell and assuming that your sequences do not wrap around)

Code:

$ foreach i (`cat ./file_of_ID_you_need`)
foreach? grep ^$i -A 3 your_sequence_file >> new_sequence_file
foreach? end

gandalf886 · 08-14-2014, 02:10 PM

perhaps this?

Code:

grep --no-group-separator -A 3 -Fxf file_2 file_1 > output

Quote:

Originally Posted by GenoMax

There are probably more elegant ways of doing this but you can try this now. With that said (in tcshell and assuming that your sequences do not wrap around)

Code:

$ foreach i (`cat ./file_of_ID_you_need`)
foreach? grep ^$i -A 3 your_sequence_file >> new_sequence_file
foreach? end

GenoMax · 08-14-2014, 02:39 PM

If sequence file is compressed then extending gandalf886's suggestion

Code:

$ zmore sample.fastq.gz | grep -A 3 -Fxf  file_of_IDs > new_sequence_file

or

Code:

$ zcat sample.fastq.gz | grep -A 3 -Fxf  file_of_IDs > new_sequence_file

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08-14-2014, 12:39 PM	#1
caputcastellae Junior Member Location: canada Join Date: Apr 2010 Posts: 1	Extract sequences from a FASTQ file based on another file I have two files: file 1: fastaq XXGB file file 2: list of a few FASTQ ID headers formatted as follows: @M01032:192:000000000-AAEFT:1:1101:10100:1004 2:N:0:1 @M01032:192:000000000-AAEFT:1:1101:10100:1004 1:N:0:1 Is there an easy way (perl?) to generate a third file with the info (including the ID headers of the targeted sequences (file 2)? Thanks!

08-14-2014, 01:03 PM	#2
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,080	There are probably more elegant ways of doing this but you can try this now. With that said (in tcshell and assuming that your sequences do not wrap around) Code: $ foreach i (`cat ./file_of_ID_you_need`) foreach? grep ^$i -A 3 your_sequence_file >> new_sequence_file foreach? end

08-14-2014, 02:39 PM	#4
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,080	If sequence file is compressed then extending gandalf886's suggestion Code: $ zmore sample.fastq.gz \| grep -A 3 -Fxf file_of_IDs > new_sequence_file or Code: $ zcat sample.fastq.gz \| grep -A 3 -Fxf file_of_IDs > new_sequence_file