how to deal with multiple pacbio and illumina files? about colormap HOT 2 OPEN

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

from colormap.

Thank you!
Xiaoting

On Wed, Sep 14, 2016 at 1:52 AM, Ehsan Haghshenas [email protected]
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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