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garber-lab / ESAT

Stripped-down version of original ESAT code
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zero counts: wrong options or ESAT not working? #31

Open ferreirafm opened 1 year ago

ferreirafm commented 1 year ago

I'm running ESAT with options below: esat -task score3p -alignments sample_sheet.tsv -geneMapping EquCab3_GenGenPred_NCBIRefSeq_All_mod.tsv -multimap normal -scPr -wExt 2500 -all -out all_samples

The reads were aligned with Cellranger so I inserted the barcodes in the read names as follows: VH00972:3:AAAL2FTHV:1:2304:71932:48820:GGTGGCTTCGGAAACG::TAGCTCCCGCGG

I also tested other combinations of ESAT options. In all of them I got an empty counts table.

In the script.log I have been getting a series of warnings as follows: WARN main umms.esat.NewESAT - location 9082 in NC_001640.1 (+) has >65535 counts. WARN main umms.esat.NewESAT - location 9092 in NC_001640.1 (+) has >65535 counts. WARN main umms.esat.NewESAT - location 9138 in NC_001640.1 (+) has >65535 counts. WARN main umms.esat.NewESAT - location 9164 in NC_001640.1 (+) has >65535 counts. INFO main umms.esat.NewESAT - Experiment IGFD BAM file /home/ferreirafm/work/colab/falko7/esat/refseq/IGFD_possorted_ge name_newreadname.bam processed in 206.412144227 sec INFO main umms.esat.NewESAT - 123412491 valid reads INFO main umms.esat.NewESAT - 2828461 invalid reads INFO main umms.esat.NewESAT - 4 BAM files processed in 835.893653349 sec INFO main umms.esat.NewESAT - 493649964 total valid reads INFO main umms.esat.NewESAT - 11313844 total invalid reads INFO main umms.esat.NewESAT - Total window count: 0

I can´t see what I'm doing wrong nor how to know if ESAT is working appropriately. Is there any way to check it. Any help is appreciated.