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sdparekh / zUMIs

zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs
GNU General Public License v3.0
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Merging demultiplexed fastq files #262

Closed MJ-Yang closed 3 years ago

MJ-Yang commented 3 years ago

Hi, thanks for providing wonderful tool !

As zUMIs prefers fastq files that are not demultiplexed, I ran merge_demutliplexed_fastq.R.

It generated 3 fastq files (R1, R2 and index reads), which seems ok.

The file that I'm concerned is reads_for_zUMIs.expected_barcodes.txt.

As I noticed, the barcodes are random characters [A-Z] of length of 8,

Which are generated by stri_rand_strings function in stringi package.

I'm wondering the use of these random characters. Can they be used as input for expected barcodes in zUMI config?

*P.S I'm dealing with Smart Seq3 libraries so I know the barcodes used in my experiment. Should I use these as input for expected barcodes in the config?

Again, thank you for your support !

cziegenhain commented 3 years ago

Hi, Yes this is intended and has been confirmed to not cause any issues.

Best, Christoph