How to use Adapter_trim

Question

[mortezasharifinia]

I want to use mirTools 2.0, but it needs to clean my data. My data is .sra file. It should be cleaned by Adapter_trim that is available on mirTools 2.0 site, but I don't know how to use Adapter_trim

Is there anyone that who could help me?

Answer 1

[Devon Ryan]

Well, the documentation states that it needs reads in fastq format, so use fastq-dump to convert the SRA file to fastq.

[Ram]

That cleaning was lightning fast! I click on edit and it is already cleaned!

[mortezasharifinia]

Actually, I converted my .sra data to fastq format by fastq-dump. Then I followed the instruction of Adapter_trim but it's not generating any file. I don't know where to save the new file or it rewrites my file.

[Devon Ryan]

Show the command that you used.

[mortezasharifinia]

perl Adapter_trim.pl -i SRR1608481.fastq -n "sample1" -f 2 >outputfile

[Ram]

.fastaq or .fastq? Also, format might be Illumina 1.3+, might wanna check on that.

[mortezasharifinia]

Sorry, misspelling that was .fastq

I will check that

[Ram]

This might help in checking: https://github.com/brentp/bio-playground/blob/master/reads-utils/guess-encoding.py

[mortezasharifinia]

How can I find out the fastaq format is in Illumina 1.0 or 1.3+?

[Ram]

Check out my comment above with the link to the guess encoding script

[mortezasharifinia]

Sorry, I've never used GitHub. How can I use your code?

[Ram]

It's not my code, it's brentp's :)

Anyway, for the short term, save this file to your machine as guess-encoding.py: https://raw.githubusercontent.com/brentp/bio-playground/master/reads-utils/guess-encoding.py

For the long term, try and explore GitHub - git is the most wonderful system for version control

[Devon Ryan]

Use the fastq file, not the sra file.