My fastQ file was delivered by the sequencing core as a combined file that has reads from two flow cell lanes. I am wondering if there's a way to split the reads from the two lanes? The downstream pipeline is Tophat-cufflinks-cuffmerge-cuffdiff.
I've also read the documentation of Tophat and did not see an option of splitting the reads in tophat, so I am asking here in this forum. thanks
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written
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newDNASeqer
2 answers
+1 for the paste
I have a pure Awk solution that is much faster. Like the above solution, let's assume that the records are blocks of 4 lines:
awk 'BEGIN {FS = ":"} {lane=$4 ; print > "lane."lane".fastq" ; for (i = 1; i <= 3; i++) {getline ; print > "lane."lane".fastq"}}' < my.R1.fastq
Using the getline command 3 times, you can read blocks of 4 lines (from the standard input, hence the <).
Can you modify the solution so that it works if the sample is sequenced on two different flowcells but, by coincidence, both runs have the same lane number? Also, my data is GZipped FASTQ.
mawk is often an alias of awk.
$ /usr/bin/awk
Usage: mawk [Options] [Program] [file ...]
Are you referring to reads from multiple lanes in one file or just interleaved R1/R2 reads from a single lane?
It should be fine to use this solution as long as nothing else has been done to original files. You can do a quick check with repair.sh from BBMap suite after separating the files to make sure the read order is retained post-split.
See that highlighted "3" in the first line? That's the lane number in the FASTQ standard. If you read in your FASTQ file and direct your reads to different output files based on that value, you'll have different FASTQ files separated by lane.
Do you need help writing the script to do that?
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is the lane in the ID for each read ? If so, you could write a simple python/perl script to do that.
Do the IDs have any distinguishing marks? (They should.) If you post a brief snippet containing a read from each lane, one of us could probably whip up a quick script or at least help you get started.