READemption

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Assign libraries for paired end data in the reademption deseq command

1

Hi, how do I assign the libraries for paired end data in the reademption deseq command? The names of my reads are like this: 1-hour-1A_p1.fq 1-hour-1A_p2.fq 1-hour-2A_p1.fq 1-hour-2A_p2.fq Where p1...

termithorbor

Unusually high memory memory usage with gene_quanti

15

Hello, I noticed that gene_quanti seems to be using a strangely high amount of memory. The command I'm running is: `reademption gene_quanti -p 4 --features 'gene,cds,region,exon' --project_path READemption_project` I'm using...

kmuench

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...

elhossary

elhossary

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...

elhossary

Hi, what are the advantages/disadvantages of using the build_fragments option for paired-end data beside being very time consuming? From my understanding it makes the analysis more precise but to what...

termithorbor

Which normalization from gene_quanti is used for Deseq2?

1

Hi, Which normalization method from the gene_quanti output is used for the Deseq2 analysis? Is there a way to change which normalization approach is used for the Desq2 analysis? Thanks...

termithorbor

Coverage is calculated based on the start and the stop position of an alignment. However, segemehl produced split reads that are very far from each other and in that case...

Tillsa

docker container without root

2

Hi, the docker image is useful although can't be used by users without root on HPC. I will suggest to change the location of miniconda to non-root directory in docker...

qiyubio

[Clarification] Why are alignments fractional?

5

Hello - thank you for engineering such a helpful tool. I'm running through the tutorial and examining the file "gene_wise_quantifications_combined.tsv", which I understand contains genewise/transcript counts along with raw counts....

kmuench