Creating Mappability Maps

Yash Prasad

unread,

Mar 6, 2024, 11:54:50 AM3/6/24

to delly-users

Hi Tobias

I am having an issue while creating mappability map.

I am trying to create it for WGS and the reference fasta is "Homo_sapiens.GRCh38.dna.chromosome.all.fasta" (3.1 GB) from "this link"

Initial steps of using dicey to chop the ref fasta and indexing worked fine.

But the step of bwa aligning and then samtools sorting :-

"bwa mem -t 8 Homo_sapiens.GRCh38.dna.chromosome.all.fasta read1.fq.gz read2.fq.gz | samtools sort -@ 8 -o srt.bam -"

is unreasonably too time consuming.

We have a PBS clustering environment and I am creating a job for 165 hours (max limit) to perform this step but still it is not completing.

Do you have an idea how can I proceed in order to get the coverage information and also perform CNV analysis for WGS sample.

Thanks for the help.

Regards

Yash

Tobias Rausch

unread,

Mar 7, 2024, 3:48:24 AM3/7/24

to Yash Prasad, delly-users

Hi,

Pre-built human mappability maps can be downloaded here: https://gear-genomics.embl.de/data/delly/

Best, Tobias

--
You received this message because you are subscribed to the Google Groups "delly-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to delly-users...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/delly-users/dce007bf-d1de-4bb7-b5dd-6f0e2a64ad71n%40googlegroups.com.

Yash Prasad

unread,

Mar 8, 2024, 2:59:42 AM3/8/24

to delly-users

Thanks for pointing out the location

PatS

unread,

Aug 1, 2024, 11:26:05 AM8/1/24

to delly-users

Hi all,

how you extract .map file from these fasta files, which are here https://gear-genomics.embl.de/data/delly/?

Thank you very much

Regads

Patricie

Dne pátek 8. března 2024 v 8:59:42 UTC+1 uživatel Yash Prasad napsal:

tr

unread,

Aug 21, 2024, 7:29:19 AM8/21/24

to delly-users

Hi,

I am not sure I understand this question. The FASTA files in the directory https://gear-genomics.embl.de/data/delly/ are pre-computed mappability maps for delly's cnv subcommand.

Best, Tobias

PatS

unread,

Aug 22, 2024, 3:37:58 AM8/22/24

to delly-users

Hi Tobias,

thank you for your answer.
I already understand. I thought that the mappability maps must be in different format, like tsv.

Best,

Patricie

Dne středa 21. srpna 2024 v 13:29:19 UTC+2 uživatel tr napsal:

Reply all

Reply to author

Forward