olechnwin

broken link in readme

2

Just want to point out the link to [https://github.com/macs3-project/MACS/blob/master/docs/advanced_usage.md](https://github.com/macs3-project/MACS/blob/master/docs/advanced_usage.md) is broken. It is the "advanced usage" link below subcommand table in readme.  Also, how can I find the advanced...

Q: filterdup result for BAMPE

1

Hi, I'm confused with `macs filterdup` result for paired-end bam files. Here are my commands and output: ``` samtools view -S -b iEF.sam.ecoli | samtools sort - -o iEF.ecoli.sorted.bam macs2...

Advanced: Call peaks using MACS2 subcommands - How to obtain fold enrichment

2

I am following the steps in [https://github.com/taoliu/MACS/wiki/Advanced%3A-Call-peaks-using-MACS2-subcommands](https://github.com/taoliu/MACS/wiki/Advanced%3A-Call-peaks-using-MACS2-subcommands). The final output will generate a file with peak location and p-values or q-values. Is there a way to get a file with...

struct.error: 'i' format

1

Hi, I'm trying to run quast but got the following error. Any help on how to solve this error is greatly appreciated. Thanks so much! ``` Running Genome analyzer... NOTICE:...

running busco with mammalian database

1

Hello, I just like to know whether it is possible to run busco analysis within quast with the mammalian database? Thanks!

Apologize if this is asked before, I tried to search but cannot find similar issue. Is there a way to convert the `p.adjust` in `enrichResult` to `-log10(p.adjust)`? I am trying...

marking duplicates

1

Is duplicate marking necessary? I saw in the readme, it was recommended to run arima mapping pipeline. However, I had already ran juicer pipeline which does not run duplicates marking....

speed up normalizeToMatrix

2

Hi, I am wondering if there is a way to speed up normalizeToMatrix or a workaround? Thank you in advance! I really enjoy using EnrichedHeatmap so far.

error 'cannot get position' when running bam2gam.sh

33

Hi, I'm trying to run bam2gam for my own dataset with the following command: `singularity exec --pwd /home/xxt050/opt/MoMI-G/scripts docker://momigteam/momig-tools:autobuild bash -x bam2gam.sh /home/xxt050/Data/A673_pacbio/HiFi/bam/A673.HiFi.hg19.sorted.md.bam /home/xxt050/Data/A673_pacbio/HiFi/vcf/momig_input.xg /vg/bin/vg ` and encountered this error:...

color for anno_enriched

2

Hi, I am wondering if there is a way to tie the anno_enriched color to the row_split? For example, below if I set ngroup1 to 10, setting anno_enriched to the...