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Demultiplexing paired-end illumina data with seprated R1 file, R2 file and index file

Hello everybody, I have a HiSeq paired-end data with three files (R1 file, R2 file and R2 index file). I need to demultiplex them before sample specific analysis and I am still looking for a tool to do that for me. I couldn't find any things. Do you have any suggestion for me? Which program can demultiplex them for me?

Many thanks

sequencing assembly
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updated by GenoMax GenoMax • written by khaled.mirzayi • khaled.mirzayi

Are you able to go back and ask your sequence provider to properly demultiplex this data? Is there a reason you have data in this format?

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written by GenoMax GenoMax

Is there a reason you have data in this format?

I've seen people asking for data like this to be able to follow this QIIME tutorial.

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written by h.mon h.mon

Thank you all for the responses. NO, It is impossible because I asked them TWO times to demultiplex the data for me and they didn't do that. I don't know why.

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written by khaled.mirzayi • khaled.mirzayi

Have your samples been prepared with standard Illumina kits? Is there anything particular about your libraries? Have the sequencing been performed a long time ago?

By the way, don't you have an R1 index file? I believe you should have two indexes (I1 + I2), or maybe just I1?

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written by h.mon h.mon

1 answer

I couldn't find any things.

My google is probably better than yours:

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written by h.mon h.mon

If this answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted. Upvote|Bookmark|Accept

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updated by GenoMax GenoMax • written by WouterDeCoster WouterDeCoster

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