Jenea I. Adams

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icon company Xing Lab @ CHOP/Penn icon location Philadelphia, PA icon location Genomics & Computational Bio Ph.D. Candidate & Penn Presidential Ph.D. Fellow @UPennGCB in the @Xinglab + @Wharton Statistics MA.

Results 3 comments of Jenea I. Adams

sc_long_pipeline.py--> ValueError: invalid contig `chr1`

Here's my output. There seem to be `chr1` reads. @HD VN:1.6 SO:coordinate @SQ SN:chr1 LN:248956422 @SQ SN:chr10 LN:133797422 @SQ SN:chr11 LN:135086622 @SQ SN:chr12 LN:133275309 @SQ SN:chr13 LN:114364328 @SQ SN:chr14 LN:107043718...

sc_long_pipeline.py--> ValueError: invalid contig `chr1`

Hello, Here's the structure of our input fastq from the ``match_cell_barcode`` step: Here's the BAM file the full pipeline starts to output: The transcript ID replaced the chromosome ID in...

sc_long_pipeline.py--> ValueError: invalid contig `chr1`

I see, thanks. With the updated input, I get a new error: > Traceback (most recent call last): > File "~FLAMES_analysis/FLAMES/python/count_tr.py", line 159, in parse_realigned_bam > bc, umi = r.split("#")[0].split("_")...