fxjonas

Dear Bowtie2 team, I am trying to find the all best alignments of true multi mapping read. I hoped this would be possible by using the -k/-a option and only...

PhyML run with constrained tree

1

Dear Stephane, I am trying to use the --constrain_file option to constrain the topology of the tree. However, I run into several problems: A) it seems to me that the...

Duplicate definition

2

Dear Samtools team, I am currently trying to quantify the number of PCR duplicates in our sequencing data. When running mark duplicates on paired-end sequencing, I noticed that it actually...

Dust and Entropy scores

3

Dear Adrian, thanks for providing this ultra-fast prinseq replacement. It seems like the definition of the Entropy and Dust scores has changed, going from 0-1 instead of 100 to 0...