Closed wodanaz closed 3 years ago
@johnbradley I forgot to mention that I have seqtk installed in my home directory and if used should be listed as a dependency. right?
What do you think?
The changes sound good to me. Do you want me to make these changes, or would you rather make the changes? If you want to make the changes I would be glad to meet and walk you through making and committing them.
I forgot to mention that I have seqtk installed in my home directory and if used should be listed as a dependency. right?
Yes. What version are you using?
I can make the commits for now.
the version of seqkt I am using is Version: 1.3-r116-dirty
Hi @johnbradley , since you pointed out the issues associated with the scrip fix-merged-bed-positions.sh to make it more general. I have been thinking a lot about it and decided that I would like to remove it from the pipeline and replaced it with a command that removes the first and last 25 nucleotides of the consensus sequence. It often has very little usable data and very lo depth that many archived sequences don't have them. So I thought on adding the following line to each consensus sequence that is generated in run-bcftools-consensus.sh
Also, I am ready to make a small modification to run-bedtools-merge.sh
in wish, I remove the need to generate an extra BED file by:
Lastly, I would like to add a floating value of the genome length to replace 29871 in create-coverage-table.sh to insert a computed value that depends upon the reference genome length. by adding:
What do you think?