Ming Tang

display function could accept filenames as well as stdin

5

Hi, I was following the post here http://jeroenjanssens.com/2015/02/19/ibash-notebook.html but the display function did not show a picture inline in the notebook. do you have any ideas of why? Thanks! Ming

the genedistance parameter https://github.com/liulab-dfci/MAESTRO/blob/master/MAESTRO/Snakemake/scATAC/Snakefile#L1166 is not used in the shell command https://github.com/liulab-dfci/MAESTRO/blob/master/MAESTRO/Snakemake/scATAC/Snakefile#L1174 Using default 10,000 bp.

according to https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02136-7 "scDblFinder achieved comparable or better accuracy than top alternatives while being the fastest method"

Hi @DongqingSun96 , can you please fix this command for multisample scATACseq? https://github.com/liulab-dfci/MAESTRO/blob/feat/multisample/MAESTRO/Snakemake/multisample/scATAC/rules/sc_atac_report.smk#L27 currently, it assumes the files are in Result/Analysis/*, but for multisample, the files are in /Result/Analysis/{sample}/* Thanks...

hi, I run phantompeakqual on my duplicates removed bam files and got an error shown in the title. later, I re-run the same command but on bam files before `samtools...

how to avoid install miniconda2 in the automated installation script?

3

I have conda installed already and do not want to install minconda2. what's the best way to install gemini and the dependencies? conda install gemini gets me an older version...

sambamba-view: unable to write to stream

2

Hi, I am using speedseq `0.1.0` to call structural variants. Most the samples are finished without error. One particular sample gave me errors below. I googled around and found [this](https://github.com/chapmanb/bcbio-nextgen/issues/1055)...

segmentation fault for speedseq sv

3

Hi Colby, I want to let you know that I am having speedseq running OK for all my samples except this one which gives me segmentation fault. I am not...

Following a discussion here https://github.com/datacarpentry/wrangling-genomics/issues/37 and my zoom call with Erin. I recently deal with SNV calling a lot and gained experience with various variant callers such as mutect (now...

[bismark-pipeline.pdf](https://github.com/crazyhottommy/DNA-methylation-analysis/files/92245/bismark-pipeline.pdf)