Trimming of XSQ or CSFASTA files

[GenomicIBK]

Hello Seqanswers community:
We did small RNA analysis using SOLiD 5500 and after putting the data in Lifescope we end up with a lot of reads from miRNAs in the unmapped file.

They look like this (for example with miRNA-1):
TGGAATGTAAAGANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN (96.248 reads)
TGGAATGTAAAGAAGTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN (28.339 reads)
TGGAATGTAAAGAAGTANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN (350.214 reads)
TGGAATGTAAAGAAGTATGTAACGCCTTGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN (10.172 reads)
TGGAATGTAAAGAAGTATGTAACGCCTTGGCCGTACAGCAGTATAACCTATAGAGANNNNNNNNNNNNNNNNNNN (39.894 reads)
Sequences in red are the reverse compliment from Adaptor T-003

Our assumption is, that these reads get excluded because of the Ns. So is there a possibility to cut these Ns in XSQ or CSFASTA format? This should be followed by an analysis with Lifescope and hopefully these reads wont be excluded any more.

Or is there a specific setting in Lifescope which allows mapping of ALL reads (regardless of the Ns) and remove the bad ones afterwards?

Any help is highly appreciated

[ashrafdallol]

GenomicIBK, did you get any help with your enquiry? I want to change the reads from 75 bp to 50 bp. is there a tool that can do this?

[GenomicIBK]

Until now, I have no solution for this problem (eg how to handle the Ns, etc).

But asking our bioinformatician, the tool cutadapt can cut XSQ or CSFASTA formatted reads.