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License: MIT License
Count Mapped Exonic Non-Duplicate (MEND) reads in an RNA Seq bam file
License: MIT License
Now outputs 3 files:
readDist.txt (same as it ever was :-)
bam_umend_qc.tsv:
input uniqMappedNonDupeReadCount estExonicUniqMappedNonDupeReadCount qc
readDist.txt 986 854.78 FAIL
bam_umend_qc.json:
{"input":"readDist.txt","uniqMappedNonDupeReadCount":986,"estExonicUniqMappedNonDupeReadCount":854.78,"qc":"FAIL"}
@hbeale @e-t-k comments? changes to variables?
maybe "qc" should become "passed": true/false to conform to json rules
mini-var-call and other analysis require the marked duplicate bam output of this pipeline vs. that of the rnaseq pipeline. See #192 for details.
This file referenced in the Dockerfile: https://downloads.sourceforge.net/project/rseqc/BED/Human_Homo_sapiens/hg38_GENCODE_v23_basic.bed.gz
no longer exists. However, I believe one can generate a bed compatible with the reference used for alignment using the table browser from UCSC.
Running the test data through the resulting container gives this error:
from bx.bitset import *
ImportError: /usr/local/lib/python2.7/site-packages/bx/bitset.so: undefined symbol: PyUnicodeUCS2_FromStringAndSize
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