BlueEidolon
commented
1 year ago ./calmeth -b KB1_pe.sorted.bam -m KB1 -Q 20 --remove_dup --coverage 4 -nC 1 --Regions 600 --step 50000 -g 60_C_idella_male_LG.fa BatMeth2::Split v2.0 Coverage and validC: 4 500, 1 Load Genome.. 60_C_idella_male_LG.fa
Longest chr: 57044276
Processing 1 out of 1. File: KB1_pe.sorted.bam, 1
start process alignment file stack smashing detected : terminated Aborted (core dumped) how to slove.
Dear Dr. Zhou,
Thank you for creating such an excellent tool.
Recently, I downloaded the methylation data from one published study. And I want to repeat the results from some analysis of this study by following their pipeline. Two main parts of the pipeline are: first, mapping reads to reference genome by Bismark; second, methylated cytosine calling using BatMeth2. However, my results (like methylation level of gene body) were quite different from those from the study.
Then I check the scripts for each step of the pipeline. Due to the large deduplicated bam filesgenerated by Bismark, I wanted to speed up the following methylated cytosine calling, so I used samtools to extract reads that aligned to different chromosomes/scaffolds, respectively (for example, one of command line is like: samtools view XXX_1_bismark_bt2_pe.deduplicated.sorted.bam chr1 > chr1_extracted.bam). Then I used calmeth in Batmeth2 for each extracted bam file to calculate methylation level.
I don’t know whether read extraction before calculating methylation level could have an influence on the downstream analysis. And I once used the bam file generated by Bismark directly to calculate methylation level, maybe due to the large size, it failed. The authors did not provide more detailed information for methylated cytosine calling using BatMeth2 in their study. Can you give me some suggestions for this problem that confused me for a long time? Thanks in advance for the help.
RuiH