dawe / scatacc Goto Github PK

When I run this code:
python ~/scatACC/bc2rg.py -w fastaq/manual_umi/prova_whitelist.tsv -i fastaq/manual_test_results_1a/8_7w_scGETseq_BC_TAAGGCGA_READ2.fq -b 8_7w_scGETseq_BC_TAAGGCGA.bam -O -k -G 8_7w_scGETseq_tn5_TAAGGCGA

The following error occurs:

Traceback (most recent call last):
File "/home/morelli/scatACC/bc2rg.py", line 114, in
main()
File "/home/morelli/scatACC/bc2rg.py", line 90, in main
header = build_header(bam_in.header, coder, options.group, options.keep_unmatched)
File "/home/morelli/scatACC/bc2rg.py", line 49, in build_header
_pl = in_header['RG'][0]['PL']
KeyError: 'PL'

Files are obtained as follows:

• _whitelist.tsv is obtained with 'umi_tools withelist'
• _READ2.fq is obtained through 'tagdust'
• the BAM file is obtained with 'bwa_mem' | 'sam_tools' sort

Right now the methods for CNA analysis are quite rough. We have log2ratio which is not properly converted into actual copy number, one may choose to keep it as is. Also, masking for centromeres/gaps should be added, as well as mask for zero-coverage regions (should be considered missing data or 0-CN regions?)