How can STAR handle reads of length zero?

[franzi]

Hi!

I hope this is not a stupid question. The STAR user manual

and google could not help me solving this problem.

I have adapter and quality-trimmed my RNAseq reads using cutadapt.

As a consequence, a few reads are trimmed to length zero.

Running STAR 2.5.2a I get the error:

"EXITING because of FATAL ERROR in reads input: short read sequence line: 1" 

and I know that this is caused by a read with length zero.

Is there a way to make STAR ignore these reads?

Thank you very much for your help !!

Best wishes,

Franzi

[Rory Kirchner]

When you run cutadapt, you can set the —minimum-length parameter to drop reads below a certain length.

Best,

Rory

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[franzi]

Thank you very much Rory!

However, with paired-end sequencing files this will discard the forward and the reverse mate

read, even if only one of the reads is too short. 

I was kinda dreaming about a way to still make use of the read in the mate file,

whenever possible. Though I could imagine that this procedure could create

some other downstream problems...   

[Alexander Dobin]

Hi Franzi,

Rory is right, the best way to deal with these reads is to filter them out.

But if you want to keep them, you could use this trick. After trimming, but before mapping, replace each empty string with a single N.

Cheers

Alex

[Franziska Witzel]

Alright. Thanks! With the choices at hand I will think about which approach to take.

Good night,

Cheers,

Franzi