tophat- paired end reads combined in one file

Question

[GR]

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

Answer 1

[Dan D]

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.

[GR]

Thanks, Does any quick script exists to do this?

[GR]

Done. Thanks!

[Dan D]

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.

[Ashutosh Pandey]

Fastq Splitter For Paired End Reads

[GR]

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