James Dalgleish

Any idea on this? I've read the previous issues that were similar, but I do have the indexes and the fa file at this point. Not sure why this error...

So, I've updated the script: `` cd ~/ABC-Enhancer-Gene-Prediction/ cd lung mkdir DNase cd DNase wget https://www.encodeproject.org/files/ENCFF023JFG/@@download/ENCFF023JFG.bam #sort and index samtools sort -l 1 -m 7G -o IMR90_DNASE_ENCFF023JFG.sorted.bam -O bam -@...

> Looks like the chromosome sizes have mixed space-and-tabs. I think changing your awk command to this will fix it: > `awk -v OFS='\t' '$1 = $1 OFS "0"' ./reference/hg38.chrom.sizes...

Also, if there is an alternative set of tools that will do the same job, I'm open to that as well.

@Manoswini-02 Maybe you have a different version of that file. I don't see that issue with the file I have on our HPC cluster. See below: ``` -bash-4.2$ gzcat /fdb/GATK_resource_bundle/hg38/Homo_sapiens_assembly38.known_indels.vcf.gz...

I would also like to mention that this is happening to me as well. One other issue is that it checks for class "seurat" when "Seurat" objects use a capital...

I just tried this method, but it doesn't recognize the format of the resulting sam file. I have removed some of the condition names for privacy purposes of those with...

I did, but I could try making SAM files instead of bam if it is helpful. Here is the syntax I used to create them. #!/bin/bash module load hicpro module...

Here is the config file: # Please change the variable settings below if necessary ######################################################################### ## Paths and Settings - Do not edit ! ######################################################################### TMP_DIR = tmp LOGS_DIR =...

Here is the directory listing, after performing the asked operations (on the deleted post, I noticed I had done ls prior to the samtools lines, hence the lack of split...