on a recent run with the original LIGR-seq dataset I'm getting the following messages when calling Aligater detect:
Use of uninitialized value $name in pattern match (m//) at /data/richard/LIGR-seq/Aligater/bin/detect.pl line 572, <> line 1087686070.
Use of uninitialized value $name in pattern match (m//) at /data/richard/LIGR-seq/Aligater/bin/detect.pl line 571, <> line 1087686070.
Use of uninitialized value $name in pattern match (m//) at /data/richard/LIGR-seq/Aligater/bin/detect.pl line 572, <> line 1087686070.
Use of uninitialized value $biotype in string eq at /data/richard/LIGR-seq/Aligater/bin/detect.pl line 560, <> line 1087686070.
So I called ./Aligater/aligater detect -p 40 --gtf GCF_000001405.39_GRCh38.p13_all.gtf --rmsk repeatMasker.hg19.slim.bed --gfam Homo_sapiens.gene_families.txt < input.sam > outputlig
So the lines refer to:
# rank biotype by..
sub biorank {
my $biotype = shift;
return 6 if ($biotype eq "misc-RNA");
return 5 if ($biotype =~ /RNA/);
return 3 if ($biotype =~ /intron/);
return 2 if ($biotype !~ /protein-coding/);
return 4;
}
So this is just for sorting and can be neglected?
Thanks
Hello Tim,
on a recent run with the original LIGR-seq dataset I'm getting the following messages when calling
Aligater detect
:So I called
./Aligater/aligater detect -p 40 --gtf GCF_000001405.39_GRCh38.p13_all.gtf --rmsk repeatMasker.hg19.slim.bed --gfam Homo_sapiens.gene_families.txt < input.sam > outputlig
So the lines refer to:
So this is just for sorting and can be neglected? Thanks