Muhammad Elhossary
Muhammad Elhossary
 The above screenshot was taken from chrome browser (any chromiuim based). The child node are there and can be selected but they are not visible. This does not apply...
The example for multi-species analysis does not work: After investigation, it seems like the Human genome input files coming from EBI cannot be parsed by Segemehl and subsequently the index...
NCBI has an extremely useful tool to download reference genomes, annotations, and reads from their repositories with much less hassle. https://www.ncbi.nlm.nih.gov/datasets/docs/v2/reference-docs/command-line/datasets/ The idea is to integrate this tool in make...
Using READemption v2.0.3 Besides the very long time it takes to build fragments, I have warnings because of the missing index files for bam files. Then errors occur due to...
Fragment building is currently part of the align command, and it is time-consuming like the aligning process. Also, It feels like the process is hanging after the aligning finishes because...
Option to filter alignments based on annotation type, for example, RNA-Seq can contain ribosomal RNA reads. if no proper rRNA depletion was done to the sample, they can be the...
Problem description: The (--crossalign_cleaning) argument in align subcommand takes a string containing 3 types of separators (comma, colon, and semicolon), one of these separators (semicolon) was used to split the...
Add support for exporting coverage as BigWig
Currently, coverage normalization is done by one factor globally across all sequences supplied to READemption, which I think logically isn't correct. The normalization should be done by a separate factor...