How to split fastq into small fastq based on barcode?

peterrjp · 12-24-2013, 01:56 AM

Dear All,
I have a big fastq file which include 34 samples. I want to split it into 34 small fastq files based on barcode sequences.
I tried to do it with the script "split_libraries_fastq" in Qiime. However, a barcode read fastq file should be used in this script. I don't know how to get this barcode read fastq file, so I can't use this script to solve the problem.
Is there any other method to solve the problem? Thank you!

Peter

wlchew · 12-24-2013, 12:13 PM

FastX-toolkit?
http://hannonlab.cshl.edu/fastx_toolkit/

Vinz · 12-30-2013, 05:54 AM

Is this MiSeq or HiSeq data?
Are you sure, the index was sequenced? If you do not specify it in the sample sheet, no index is sequenced. Then there is no way to determine the samples and split the fastq afterwards.
Open the fastq with an appropriate text viewer and see if barcode information is present in the header of each read.

GenoMax · 12-30-2013, 04:06 PM

Two things you need to clarify. Is the barcode "inline" (part of the sequence read) or was it sequenced separately (as in Illumina multiplexing)?

As Vinz said above if you are not sure then you can "cat" or "zcat" the sequence file (pipe through "more") and then post a few sequences here so someone can help.

GW_OK · 12-30-2013, 06:24 PM

Quote:

Originally Posted by GenoMax

As Vinz said above if you are not sure then you can "cat" or "zcat" the sequence file (pipe through "more") and then post a few sequences here so someone can help.

Oh, man, use 'less' or 'zless' (press 'q' to return to command line). Way better than 'cat' piped through 'more'.

acoada · 12-30-2013, 07:06 PM

try perl.
you can store barcode list in a hash.

peterrjp · 12-30-2013, 07:25 PM

Dear All,
Thank you for your replies! I have solve the problem with the FASTX-ToolKit software. Besides, I also found the way to get a barcode.fastq with the script split_libraries_fastq.py (http://qiime.org/tutorials/extractin...astq_data.html).

Peter

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12-24-2013, 01:56 AM	#1
peterrjp Junior Member Location: CIB. China Join Date: May 2013 Posts: 2	How to split fastq into small fastq based on barcode? Dear All, I have a big fastq file which include 34 samples. I want to split it into 34 small fastq files based on barcode sequences. I tried to do it with the script "split_libraries_fastq" in Qiime. However, a barcode read fastq file should be used in this script. I don't know how to get this barcode read fastq file, so I can't use this script to solve the problem. Is there any other method to solve the problem? Thank you! Peter

12-24-2013, 12:13 PM	#2
wlchew Junior Member Location: MA Join Date: Jun 2013 Posts: 3	FastX-toolkit? http://hannonlab.cshl.edu/fastx_toolkit/

12-30-2013, 05:54 AM	#3
Vinz Member Location: Germany Join Date: Dec 2010 Posts: 80	Is this MiSeq or HiSeq data? Are you sure, the index was sequenced? If you do not specify it in the sample sheet, no index is sequenced. Then there is no way to determine the samples and split the fastq afterwards. Open the fastq with an appropriate text viewer and see if barcode information is present in the header of each read.

12-30-2013, 04:06 PM	#4
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,091	Two things you need to clarify. Is the barcode "inline" (part of the sequence read) or was it sequenced separately (as in Illumina multiplexing)? As Vinz said above if you are not sure then you can "cat" or "zcat" the sequence file (pipe through "more") and then post a few sequences here so someone can help.

12-30-2013, 07:06 PM	#6
acoada Junior Member Location: China Join Date: Dec 2013 Posts: 8	try perl. you can store barcode list in a hash.

12-30-2013, 07:25 PM	#7
peterrjp Junior Member Location: CIB. China Join Date: May 2013 Posts: 2	Dear All, Thank you for your replies! I have solve the problem with the FASTX-ToolKit software. Besides, I also found the way to get a barcode.fastq with the script split_libraries_fastq.py (http://qiime.org/tutorials/extractin...astq_data.html). Peter