Question: bcl2fastq-V2 How to skip some line
0
gravatar for BioRyder
4.5 years ago by
BioRyder170
India
BioRyder170 wrote:

Hello All,

I have one eight lane HiSeq-4000  flow cell data.I want to demultiplex only lane 5,6,7,8 and skip other lanes.I made a sample sheet with only lane 5,6,7 & 8 and processed the bcl2fastq by the following command. But it generate lane 5,6,7 & 8 lane data laong with Undetermined fastq file of lane 1,2,3 & 4.It is time more time & space consuming process.Please let me know that Is there any way to skip the unwanted line ? So we can save time and space while doing bcl2fast.

command Used : bcl2fastq --input-dir 151112_K00155_0019_BH573GBBXX/Data/Intensities/BaseCalls/ --runfolder-dir 151112_K00155_0019_BH573GBBXX/ --sample-sheet Samplesheet.csv  --output-dir unaligned --use-bases-mask Y*,I8n,Y* --barcode-mismatches 1 -l DEBUG &

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ADD COMMENTlink modified 2.4 years ago by Biostar ♦♦ 20 • written 4.5 years ago by BioRyder170
2

Hello Devon / h.mon

--tiles s_[5-8] worked fine.Thank you so much for the help

ADD REPLYlink modified 6 months ago by RamRS27k • written 4.5 years ago by BioRyder170

If we need only 4 & 6 lane, then what will be the option. I have tried with --tiles s_[4,6]. But it return error. Please can you suggest me?

ADD REPLYlink modified 6 months ago by RamRS27k • written 4.5 years ago by BioRyder170

I got the answer. It worked with --tiles s_[46]

ADD REPLYlink modified 6 months ago by RamRS27k • written 4.5 years ago by BioRyder170
4
gravatar for h.mon
4.5 years ago by
h.mon29k
Brazil
h.mon29k wrote:

Are you using bcl2fastq2? If so, I think you could use the --tiles parameter:

--tiles s_[5-8]

edit: I've updated my answer according to Devon Ryan comment bellow, previously it was --tiles s[5-8]

ADD COMMENTlink modified 6 months ago by RamRS27k • written 4.5 years ago by h.mon29k
2

I think it's --tiles s_[5-8], but my thoughts exactly.

ADD REPLYlink written 4.5 years ago by Devon Ryan95k

iIf we need only 4 & 6 lane, then what will be the option. I have tried with --tiles s_[4,6]. But it return error. Please can you suggest me?

ADD REPLYlink modified 6 months ago by RamRS27k • written 4.5 years ago by BioRyder170
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