Closed tmhmxg59 closed 5 years ago
Hi,
xHLA only works with hg38 reference.
The get-reads-alt-unmap.sh script needs to be used when you have a BAM aligned on hg38 reference with alt contigs.
Best, Astrid
Conversion from 37 to 38 worked for me for one bam. I used: docker run -v ~/bams:/opt/bin/myData -it --entrypoint=/bin/bash humanlongevity/hla to open a container with my local directory /bams bound to /opt/bin/myData.
I did have to remove the memory detection part of the script as it gave an error at line 17. And add the fna as @cjieming noted.
On a second data set, though, I'm loosing about half of the reads somewhere in the script. My first go I added a few reads as expected. The only thing I can think of is: when I ran the first time I was using a 37 bam PrintRead to chr6. The first step in the script is to trim, though, so I'm not sure what the issue is.
Second data set had chromosome names as number only, so modified get-reads-alt-unmap.sh to 6 instead of chr6.
I'm struggling to get typing information from hg19 aligned bams. I think I'd like to run get-reads-alt-unmap.sh in the docker container - I don't have all the dependencies on my machine.
I think I need to change the entrypoint, but I'm not sure the syntax. The coordinates in the .sh script appear to cover all genes in both references.
I tried several variations of: $docker run -itv
pwd
:pwd
pwd
-w humanlongevity/hla --entrypoint /bin/bash ls docker: invalid reference format: repository name must be lowercase. See 'docker run --help'.But doesn't seem like I've successfully changed the entrypoint.