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sfu-compbio / colormap

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how to deal with multiple pacbio and illumina files? #2

Open xthua opened 8 years ago

xthua commented 8 years ago

Hi, everyone, the command to correct the read is : ./runCorr.sh However, it did not mention that how to deal it with multiple pacbio and illumina files? especially, the paired-end files contained two files. is there any advices? Thanks very much!

Best wishes, Xiaoting

haghshenas commented 8 years ago

Hi Xiaoting, Sorry for delay, I was travelling in the past week. At the moment, CoLoRMap expects only a single file for pacbio and illumina reads. So for now, you can concatenate the reads into one file. About the paired-end files, runCorr.sh does not use the paired-end information. But runOEA.sh expects the paired-end reads in interleaved/interlaced format. For now, you can use fastUtils shuffle program (in the bin folder) to generate the interleaved/interlaced file from the separated paired-end files. However, I am working on a python wrapper for CoLoRMap that takes care of all different cases such as multiple read files and separated paired-end files. Thank you for your feedback.

Ehsan

xthua commented 8 years ago

Thank you! Xiaoting

On Wed, Sep 14, 2016 at 1:52 AM, Ehsan Haghshenas notifications@github.com wrote:

Hi Xiaoting, Sorry for delay, I was travelling in the past week. At the moment, CoLoRMap expects only a single file for pacbio and illumina reads. So for now, you can concatenate the reads into one file. About the paired-end files, runCorr.sh does not use the paired-end information. But runOEA.sh expects the paired-end reads in interleaved/interlaced format. For now, you can use fastUtils shuffle program (in the bin folder) to generate the interleaved/interlaced file from the separated paired-end files. However, I am working on a python wrapper for CoLoRMap that takes care of all different cases such as multiple read files and separated paired-end files. Thank you for your feedback.

Ehsan

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