paired end reads as input

[junjieahaha]

Can i use paired end fastq as input files? Or i should probably merge two paired end fastq to a single fastq file?

[gkudla]

Yes, you should merge the two ends together before running hyb.

Greg

On Fri, Oct 13, 2017 at 10:03 AM, junjieahaha notifications@github.com wrote:

Can i use paired end fastq as input files? Or i should probably merge two paired end fastq to a single fastq file?

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[junjieahaha]

Another question:how to skip the steps of preprocessing reads, for example, type in 'hyb detect align=bowtie2 in=data.fastq db=hOH7' it will automatically completes to 'in=data.fastq id=data format=fastq code= miss=0 qc=flexbar qual=33 link=TGGAATTCTCGGGTGCCAAGGC min=4 len=17 trim=0 filt=0 pc=0 align=bowtie2 db=hOH7 word=11 eval=0.1 ref= anti=0 type=all fold=UNAfold pref=mim hval=0.1 hmax=10 gmax=4'. For the reads ars already clean data.

[gkudla]

try: qc=none

On Fri, Oct 13, 2017 at 3:46 PM, junjieahaha notifications@github.com wrote:

Another question:how to skip the steps of preprocessing reads, for example, type in 'hyb detect align=bowtie2 in=data.fastq db=hOH7' it will automatically completes to 'in=data.fastq id=data format=fastq code= miss=0 qc=flexbar qual=33 link=TGGAATTCTCGGGTGCCAAGGC min=4 len=17 trim=0 filt=0 pc=0 align=bowtie2 db=hOH7 word=11 eval=0.1 ref= anti=0 type=all fold=UNAfold pref=mim hval=0.1 hmax=10 gmax=4'. For the reads ars already clean data.

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[junjieahaha]

Thank you. ^-^