tophat- paired end reads combined in one file
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8.3 years ago
RT ▴ 360

Hi All,

Just a quick question re tophat- How does tophat handles the paired-end data when both the reads (left and right) are in one file. I mapped this data (still running) using tophat without separating the paired-end reads in two different files. Will top handle this or I should separate the files?

Thanks,RT

RNA-seq tophat • 5.3k views
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8.3 years ago
Dan D 7.3k

You should separate the FASTQ reads into two files for Tophat. It will not recognize them as paired-end reads if they are together in the same file.

From the manual:

##Using TopHat

Usage: `tophat [options]* <genome_index_base> <reads1_1[,...,readsN_1]> [reads1_2,...readsN_2]`

When running TopHat with paired reads it is **critical** that the `*_1` files an the `*_2` files appear in separate comma-delimited lists, and that the order of the files in the two lists is the same.
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Thanks, Does any quick script exists to do this?

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Done. Thanks!

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Just out of curiosity, which tool did you use to successfully accomplish this? I haven't had to do such a thing yet, but I'm sure I will at some point and it would be nice to know what works.

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Deedee, I wrote my own python script. I tried to use grep but it does not print the quality line in the new file. I don't know why.

grep -A 3 '/1' test.fastq > test_leftreads.fastq
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