Open markmcdowall opened 5 years ago
Thanks for your reporting.
I re-checked the codes, and didn't find any code convert "." to "_" for chromosome names. As BS-Seeker2 is wrapping above bowtie/bowtie2, it might be the bowte/bowtie2 build-in function.
Also you're welcomed to give more details on which step and examples of chr names you use.
Best, Weilong
Hi Weilong,
Thank you for getting back to me.
I started digging through the code and it looks like the change happens as part of the read_fasta()
function in the bam_utils (https://github.com/BSSeeker/BSseeker2/blob/master/bs_utils/utils.py). There is a regex (sanitize_seq_id
) to convert all values that are not A-Z
, a-z
or 0-9
to a _
(lines 275 and 286).
For example the chromosome name CM001012.2
(mouse chromosome 19 as supplied by ENA - https://www.ebi.ac.uk/ena/data/view/CM001012). This gets converted from CM001012.2
to CM001012_2
, which makes it impossible to view the bam file on something like JBrowse if the name is loaded as CM001012.2
.
Adding .
to the list of non-removed characters might be enough to prevent this and not affect names of files in a system.
Cheers,
Mark
@markmcdowall Great thanks for figuring out this bug. And the code is fixed in the new release (v2.1.7).
Best, Weilong
Thanks Weilong,
I'll update my installation.
Cheers,
Mark
Hi,
When running the indexing steps over genomes where the chromosome name includes a
.
, these get converted to an underscore. I have wrapped the steps as part of a pipeline and wish to convert the output to a bigwig file, but this fails due to the name changes.Is it possible to prevent the renaming of the chromosomes, or is there a specific reason why there is renaming?
Cheers,
Mark