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Illumina / interop

C++ Library to parse Illumina InterOp files
http://illumina.github.io/interop/index.html
GNU General Public License v3.0
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Index with # of reads information #325

Closed Nitin123-4 closed 10 months ago

Nitin123-4 commented 11 months ago

Hi team,

I am using this tool for the first time. From the example MiSeq run or from any Novaseq run, I want the list of indexes sequenced with total reads.

For Example: ATGCATCG+GCTAGCAG : 4576234 Can you please help me to get the python code for it?

Thanks.

ezralanglois commented 11 months ago

I think you are looking for this https://github.com/Illumina/interop/blob/master/docs/src/Tutorial_04_Indexing_Metrics.ipynb

Be aware that the IndexMetricsOut.bin is not produced by RTA. It is produced by the bcl conversion software. On some systems, it needs to be moved into the InterOp directory manually if it is not already there.

Nitin123-4 commented 11 months ago

Thanks for your response. I ran it and see that it gives all the indexes which are there in SampleSheet.csv.

Is it possible to get the Index 1 (I7),Index 2 (I5) ,% Reads Identified (PF) for all the sequenced indexes.

Basically I am looking for all the indexes sequenced or maybe top 1000.

Thanks.

ezralanglois commented 11 months ago

Do you mean the top unknown bar codes? If so, those are not stored in the InterOp file.

Nitin123-4 commented 11 months ago

Okay, Basically what I wanted to look for if I can get top 1000 barcodes and reads or % Reads Identified (PF) for them before even doing demultiplexing. This way I can use this information for some checks.

So basically if we can get All or top 1000 indexes which shows reads in the run.

ezralanglois commented 11 months ago

Do those barcodes all show up in the samplesheet?

Nitin123-4 commented 11 months ago

No.

Is it possible to get even if sample sheet is not there? I mean from the run folder only can we get this information? Thanks.

ezralanglois commented 11 months ago

InterOp requires the IndexMetricsOut.bin to be in the InterOp subdirectory of the run folder. IndexMetricsOut.bin only contains information on the barcodes in the samplesheet

Nitin123-4 commented 11 months ago

Okay.

Is there any way you recommand to get the information?

Thanks for your quick response.

ezralanglois commented 11 months ago

Not with this library.

Check out this page: https://support.illumina.com/sequencing/sequencing_software/bcl-convert/documentation.html

tamuanand commented 1 month ago

I think you are looking for this https://github.com/Illumina/interop/blob/master/docs/src/Tutorial_04_Indexing_Metrics.ipynb

Be aware that the IndexMetricsOut.bin is not produced by RTA. It is produced by the bcl conversion software. On some systems, it needs to be moved into the InterOp directory manually if it is not already there.

Hi @ezralanglois

The above python notebook link is not working. Request you to share the correct link

Thanks