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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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Error in alldt[[i]][[2]] : subscript out of bounds Calls: bindList #320

Closed parichitran closed 2 years ago

parichitran commented 2 years ago

Dear chrishtop, I am so much greatful to you for making such a wonderful tool.I am currently using your zUMIs and your allele_level_expression script for my celseq2 data.

In order to understand and validate the "allele_level_expression" script.I ran the smartseq-3 mouse data below

E-MTAB-8735 - Single-cell RNA counting at allele- and isoform-resolution using Smart-seq3

Read 1 ->Smartseq3.Fibroblasts.NovaSeq.R1.fastq.gz Read 2 ->Smartseq3.Fibroblasts.NovaSeq.R2.fastq.gz Read 3->Smartseq3.Fibroblasts.NovaSeq.I1.fastq.gz Read 4->Smartseq3.Fibroblasts.NovaSeq.I2.fastq.gz

For barcode: I extracted barcode list from this file Smartseq3.Fibroblasts.sample_annotation.txt

I ran zUMIs same as your https://github.com/sandberg-lab/Smart-seq3/blob/master/allele_level_expression/mouse_cross.yaml but without '--clip3pAdapterSeq' parameter I had used the N-masked mouse genome generated with SNPsplit using mouse dbsnp.

Barcode file barcode.txt

Yaml & terminal output yamlterminaloutput.txt

Thanks in advance

parichitran commented 2 years ago

I reran zUMIs from Counting step as below 258 issues work around, who also faced same error.zUMIs ran successfully.I feel this is a memory based error.Any information regarding this are welcome.Anyway this is the work around for this problem.I am closing it here

https://github.com/sdparekh/zUMIs/issues/258.