Question: tophat- paired end reads combined in one file
2
gravatar for RT
5.4 years ago by
RT340
European Union
RT340 wrote:

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 mapping tophat • 4.5k views
ADD COMMENTlink modified 5.4 years ago by Dan D7.0k • written 5.4 years ago by RT340
6
gravatar for Dan D
5.4 years ago by
Dan D7.0k
Tennessee
Dan D7.0k wrote:

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.
ADD COMMENTlink modified 3 months ago by RamRS25k • written 5.4 years ago by Dan D7.0k

Thanks, Does any quick script exists to do this?

ADD REPLYlink written 5.4 years ago by RT340

Done. Thanks!

ADD REPLYlink written 5.4 years ago by RT340

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.

ADD REPLYlink written 5.4 years ago by Dan D7.0k
1

Fastq Splitter For Paired End Reads

ADD REPLYlink modified 3 months ago by RamRS25k • written 5.4 years ago by Ashutosh Pandey12k

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
ADD REPLYlink modified 3 months ago by RamRS25k • written 5.4 years ago by RT340
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