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

Question

[khaled.mirzayi]

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

[GenoMax]

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?

[h.mon]

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.

[khaled.mirzayi]

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.

[h.mon]

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?

Answer 1

[h.mon]

I couldn't find any things.

My google is probably better than yours:

• https://github.com/HaisiYi/Bayexer
• https://github.com/grenaud/deml
• https://github.com/merenlab/illumina-utils
• http://qiime.org/scripts/split_libraries_fastq.html

[khaled.mirzayi]

Wow absolutely is better. thank you

[WouterDeCoster]

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