TopHat: how to use paired-end reads without partner

[nike00]

Dear all,

I'm working with paired-end reads (2x70b) from Illumina.
My question is very basic:
before using TopHat for mapping,
I filter out the reads depending on the quality,
then I check reads still paired.

Now, can I use the reads without their partner (because of the quality) as single reads? or is it better not to use them?

Thanks,
nike00

[ttnguyen]

Probably you don't need to filter out the low quality reads because Tophat can handle them.

[gringer]

Another option is to use masking if you want to make sure that reads definitely won't be used for mapping. This means the ends will match up when using a paired-end analysis programs that processes the reads based on read number (rather than read label). The fastx-tools package has a program 'fastq_masker' that will mask out low quality reads without removing them entirely. The fastx-tools use ascii offset 64 by default for quality scores, but this can be changed by the [undocumented] -Q option, if necessary:

fastq_masker -Q 33 -i ~/illuminadata/s_7_1_1106.fastq > masked_s_7_1_1106.fastq