Open grafitos opened 2 years ago
Hi,
Given the BED specification (https://samtools.github.io/hts-specs/BEDv1.pdf), page 3, apostrophe character can be used in name field.
Creating the input file /tmp/input:
SAMPLE_1 XXX_exon_11 chr1 16262627 16262627 T G 6650 56 3867 2716 35 21 T/C 0.0084 2;2 5.9 1 32.2 1 0.58923 0.85431 60 10.2 0.0084 0 0 2 1 1.3 51 6066 AAAAAAAAAAA TTTTTTTTTT chr1:16254573-16262773 SNV 0 0
And running cat /tmp/input | teststrandbias.R is OK.
cat /tmp/input | teststrandbias.R
But with this input file:
SAMPLE_1 XXX_exon_11_3'_UTR chr1 16262627 16262627 T G 6650 56 3867 2716 35 21 T/C 0.0084 2;2 5.9 1 32.2 1 0.58923 0.85431 60 10.2 0.0084 0 0 2 1 1.3 51 6066 AAAAAAAAAAA TTTTTTTTTT chr1:16254573-16262773 SNV 0 0
Running cat /tmp/input | teststrandbias.R produces no output.
Hi,
Given the BED specification (https://samtools.github.io/hts-specs/BEDv1.pdf), page 3, apostrophe character can be used in name field.
Creating the input file /tmp/input:
SAMPLE_1 XXX_exon_11 chr1 16262627 16262627 T G 6650 56 3867 2716 35 21 T/C 0.0084 2;2 5.9 1 32.2 1 0.58923 0.85431 60 10.2 0.0084 0 0 2 1 1.3 51 6066 AAAAAAAAAAA TTTTTTTTTT chr1:16254573-16262773 SNV 0 0And running
cat /tmp/input | teststrandbias.Ris OK.But with this input file:
SAMPLE_1 XXX_exon_11_3'_UTR chr1 16262627 16262627 T G 6650 56 3867 2716 35 21 T/C 0.0084 2;2 5.9 1 32.2 1 0.58923 0.85431 60 10.2 0.0084 0 0 2 1 1.3 51 6066 AAAAAAAAAAA TTTTTTTTTT chr1:16254573-16262773 SNV 0 0Running
cat /tmp/input | teststrandbias.Rproduces no output.