Pre processing of Illumina data

[tusharbiot]

Hi all!

Though there have been many similar posts, but to have an updated (and more recent) thought, hence I am posting it again.

I have some Illumina GAIIX paired end data in two separate files (with their suffix as _1 and _2). Before putting them for assembly, I need to perform certain pre processing of these file to alleviate its quality (probably FASTQ MASKER by quality control on GLAXY web tools). My query is " Should I join these paired end data first and then go on with the quality treatments OR should I just perform the quality treatment and then join the two files.

Thanks in advance
Any help will be deeply appreciated.

[ians]

Originally Posted by tusharbiot

My query is " Should I join these paired end data first and then go on with the quality treatments OR should I just perform the quality treatment and then join the two files.

what do you mean when you say, "join"?

[tusharbiot]

With join I meant should I combine the two files into one (basically the tool I am using just concatenates the two sequences from a single locus/index).

[faozhi]

I know I didn't combine them during trimming based on qual...

[tusharbiot]

Originally Posted by faozhi

I know I didn't combine them during trimming based on qual...

faozhi, so that would mean you combined them after the quality screening.

[SES]

Originally Posted by tusharbiot

Hi all!

Though there have been many similar posts, but to have an updated (and more recent) thought, hence I am posting it again.

I have some Illumina GAIIX paired end data in two separate files (with their suffix as _1 and _2). Before putting them for assembly, I need to perform certain pre processing of these file to alleviate its quality (probably FASTQ MASKER by quality control on GLAXY web tools). My query is " Should I join these paired end data first and then go on with the quality treatments OR should I just perform the quality treatment and then join the two files.

Thanks in advance
Any help will be deeply appreciated.

It actually makes no difference at all, but you don't want to create extra work for yourself. With that in mind, you should probably trim the files separately, that way it will be easy to identify which read pairs were retained after the trimming and which reads should be treated as single-end.