ASM calling Error for ass and asr Allele Specific methylation analysis.

[AbRawoof]

Hi Weilong,

I am trying to analyze allele specific methylation and while performing analysis using below parameter
$ cgmaptools asm -r refgenome.fa -b sample1_sorted.bam -l sample1_bayes.vcf -o sample1-CG_ASM-Sites -t CG -m ass -d 5

it gave following error:
" substr outside of string at /home/u/cgmaptools/bin/ASM line 573.
Use of uninitialized value in string eq at /home/u/cgmaptools/bin/ASM line 275."
I am using perl v5.30.0.

Thank you,
Abdul Rawoof

[guoweilong]

The ASM.pl has been updated, and you can try with the new code: https://github.com/guoweilong/cgmaptools/blob/master/src/ASM.pl Weilong At 2022-07-24 01:15:27, "AbRawoof" ***@***.***> wrote: Hi Weilong, I am trying to analyze allele specific methylation and while performing analysis using below parameter $ cgmaptools asm -r refgenome.fa -b sample1_sorted.bam -l sample1_bayes.vcf -o sample1-CG_ASM-Sites -t CG -m ass -d 5 it gave following error: " substr outside of string at /home/u/cgmaptools/bin/ASM line 573. Use of uninitialized value in string eq at /home/u/cgmaptools/bin/ASM line 275." I am using perl v5.30.0. Thank you, Abdul Rawoof — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[AbRawoof]

Thanks Weilong,

These are really quite useful scripts.

Also, running asm for even 700Mb input vcf files with 40Gb bam files is bit lengthy process.
It is taking much of time (2-3 days) to complete a single context analysis.
Is there any way to speed up the analysis?

Thank you,
Abdul Rawoof

[guoweilong]

Thanks for your questions. Many of the DNA methylation analysis could be time-costing. For the case you mentioned, you may try to split the large BAM files into mutilple independent BAM files by chromosomes, and the run the command in parallele. This way would definitely save the time! Best, Weilong At 2022-07-26 21:43:55, "AbRawoof" ***@***.***> wrote: Thanks Weilong, These are really quite useful scripts. Also, running asm for even 700Mb input vcf files with 40Gb bam files is bit lengthy process. It is taking much of time (2-3 days) to complete a single context analysis. Is there any way to speed up the analysis? Thank you, Abdul Rawoof — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: ***@***.***>

[AbRawoof]

Dear Weilong,
Splitting bam files by chr would definitely reduce the analysis time.. Thanks for your suggestions.

Best,
Abdul Rawoof