Convert paired-end, longer reads to single-end, shorter reads

[mlodato]

Hi,
Possibly a very dumb question, but if I have a dataset of paired-end, 150bp reads, but a computational tool that is formatted to analyze single-end 50bp reads. I am wondering if it is practically feasible to only consider 1 end for each read, and clip that read to 50 bp, and use it. Also, is it logical to do so, in other words am I missing some reason why this is a bad idea?

Thanks for any help!

[Brian Bushnell]

This depends on what you want to use the data for. The approach you suggest is certainly feasible to force an old tool to handle new data, but at the expense of discarding a huge amount of useful data and basically undoing 5 years of advancement in sequencing technology. The best approach would usually be to find or make a tool that is flexible enough to accept and utilize modern data, if you want the most accurate possible answer. What does the tool do?

[mlodato]

Thanks, I've thought about the issues you've raised and agree with you. I want to use this tool (http://www.nature.com/nprot/journal/....2012.039.html), which measures copy number. I will be using this analysis as a QC on low-coverage sequencing to pick out bad samples before high-coverage sequencing, so throwing out lots of data would not be the end of the world.

[proux]

This is my first post, and I have the same question - although the tool I have in mind is the newer qDNAseq, but it seems to also want single end 50bp reads. https://www.bioconductor.org/package...l/QDNAseq.html

[proux]

i guess this should allow at least the split into single ended

http://bedtools.readthedocs.org/en/latest/content/tools/bamtofastq.html

[GenoMax]

This is my first post, and I have the same question - although the tool I have in mind is the newer qDNAseq, but it seems to also want single end 50bp reads. https://www.bioconductor.org/package...l/QDNAseq.html

Where does it say that it requires 50 bp reads? I looked through the reference manual. Perhaps I missed that part.

[GenoMax]

i guess this should allow at least the split into single ended
http://bedtools.readthedocs.org/en/l...amtofastq.html

If data you are looking at is paired-end then split it and use just one end (if that is all you need). Generally R1 (first) read would be one to use.

[proux]

thanks. 50 bp reads is the only input accepted in the galaxy version. It is not explicitly stated in the R package, but it is what they used in the paper for their own data, and they truncated 1000 genomes data to the first 50 bp