Closed splaisan closed 5 years ago
I found it, my chromosome names (from Ensembl) had a name containing a space and the word dna as created by the UCSC Kent tool faSize. I replaced this step by samtools faidx | cut -f1,2 to produce a valid file.sizes
# clean reference fasta file (names with space or comments)
bioawk -c fastx '{print ">"$name; print $seq}' ${infile} \
> ${outdir}/${infile}
# create reference size list
echo "# creating reference size list"
samtools faidx ${outdir}/${infile} \
&& cut -f 1,2 ${outdir}/${infile}.fai \
> ${outdir}/${pref}.sizes
eg '>2L dna:chromosome chromosome:BDGP6:2L:1:23513712:1 REF' => '2L dna' This let to adding a column in the output and shift data around now fixed!
Hi, just for those who also had this problem. I encountered the exact same problem. The faSize
gave me the correct file. But the wig file has 1 dna
as chromosome name.
My solution is to delete the dna
from wig file (sed "s/ dna//" test.wig > test2.wig
). Then the wigToBigWig
works fine.
I used the latest beta from sourceforge (1.423) to produce a mappability track for the latest Drosophila genome build.
My code used to work for other genomes in the past but now fails producing the final BigWig with
error: # converting to BigWIG strange var=val pair line 1 of ./BDGP6.94-mappability/BDGP6.94_150.wig
what is wrong with this wig that makes wigToBigWig so unhappy?
does this have to do with the chromosome naming of droso? or with the variableStep?
Thanks for any hint.
Stephane
my simplified code