software to cut adaptor

[tiffany081126]

Hi all,

Since I am new here, I am not familiar with the data analysis from SOLiD platform.

Yesterday, I was told to cut the reads(50bp) into 30bp or shorter before performing mapping, otherwise I won't get anything since almost half of the read is from adaptor.

So, could you give me some suggestions about which software can do this work and what the adaptor should I prepare before?

Thanks a lot.

BTW, I am focus on miRNA sequencing. And yesterday I used PerM to mapping the reads with the genome reference, but I only got 0.03% mapping result.

[ECO]

You need to know how the library was constructed to determine where to trim. Ideally whoever generated the library would know this information.

[tiffany081126]

I just the person who make the construction, and already have the adaptor sequence, but what I don't know is that which software can do the trimming, or should I write a script with Perl to do so?

[Simon Anders]

If you want to write a script yourself, our HTSeq framework might be useful. It has functions to partially match an adapter sequence to a read and trim the read this way.

Here is how this would roughly look like:

import HTSeq

file_in = "yeast_RNASeq_excerpt_sequence.txt"
file_out = "trimmed.fastq"

adapter = HTSeq.Sequence( "ACCGTA" )
adapter_rc = adapter.get_reverse_complement()

fout = open( file_out, "w" )
for read in HTSeq.FastqReader( file_in ):
   read = read.trim_right_end( adapter )
   read.write_to_fastq_file( fout )
fout.close()

This is now for Sanger FASTQ, but I guess it should work with CSFASTQ as well.

Simon

[tiffany081126]

Hi, Simon

I was wondering whether I should change the format of csfasta to fastq before trimming, while your suggestion definitely helps me a lot.

Thanks a lot.

Tiffany

[Tina]

If you have the adapter sequence with you then try using the program fastx_clipper which is a part of FASTX-toolkit.

http://hannonlab.cshl.edu/fastx_toolkit/commandline.html

Hope this helps.

[zee]

Tiffany, my group are actively developing a new aligner, NovoalignCS, for colorspace and this would be a great feature to have. In fact we already have it in our NT space aligner.

We currently support iterative read trimming in cases where the adaptor is not known.

Are your adaptors in nucleotide space? I would be interested in obtaining some test data if that's possible and we could provide you with a beta version of the working program.

Hi all,

Since I am new here, I am not familiar with the data analysis from SOLiD platform.

Yesterday, I was told to cut the reads(50bp) into 30bp or shorter before performing mapping, otherwise I won't get anything since almost half of the read is from adaptor.

So, could you give me some suggestions about which software can do this work and what the adaptor should I prepare before?

Thanks a lot.

BTW, I am focus on miRNA sequencing. And yesterday I used PerM to mapping the reads with the genome reference, but I only got 0.03% mapping result.

[Chipper]

If you don't want to use another aligner you could just make a new file like this:
awk '{print substr($0,0,21)}' filename.csfasta > filename.csfasta.20

else try bowtie, you can either set it to use a short seed or trim ends.

[tiffany081126]

If you have the adapter sequence with you then try using the program fastx_clipper which is a part of FASTX-toolkit.

http://hannonlab.cshl.edu/fastx_toolkit/commandline.html

Hope this helps.

Tina,

Thanks a lot. I am using this toolkit these days.

Tiffany

[tiffany081126]

Tiffany, my group are actively developing a new aligner, NovoalignCS, for colorspace and this would be a great feature to have. In fact we already have it in our NT space aligner.

We currently support iterative read trimming in cases where the adaptor is not known.

Are your adaptors in nucleotide space? I would be interested in obtaining some test data if that's possible and we could provide you with a beta version of the working program.

zee,

Thanks a lot. But I will try the toolkit first. Connect you later if it doesn't work.

Tiffany

[tiffany081126]

If you don't want to use another aligner you could just make a new file like this:
awk '{print substr($0,0,21)}' filename.csfasta > filename.csfasta.20

else try bowtie, you can either set it to use a short seed or trim ends.

Chipper,

But I think it's too blind to do so. Any other good ideas to trim it according to the known sequence of the adaptor?

Nevertheless, thanks a lot for your suggestion.

Tiffany

[patternist]

mirTools web site provides a perl script for adaptor trimming.

http://centre.bioinformatics.zj.cn/mirtools/adaptortrim.php

[tiffany081126]

mirTools web site provides a perl script for adaptor trimming.

http://centre.bioinformatics.zj.cn/m...daptortrim.php

Thanks, patternist!

And I find this info is very useful for me.

Thanks a lot.

Tiffany

[mmartin]

I see requests for an adapter-removal software quite often and since fastx_clipper does not seem to be able to deal with color space data, I have now made the tool we use in our group available for download. Please have a look https://code.google.com/p/cutadapt/ and write me if you have any questions.

[tiffany081126]

I see requests for an adapter-removal software quite often and since fastx_clipper does not seem to be able to deal with color space data, I have now made the tool we use in our group available for download. Please have a look https://code.google.com/p/cutadapt/ and write me if you have any questions.

Thanks very much, but I have solve the problem by a script of my senior.

Thansks again.

Tiffany