lmanchon

--Hi, do you think to update a patch for MISO because it requires only fixed read lengths and after trimming step the reads have different lengths. thank you,

UMI analysis with XT-HS library

4

Hello, I use the SSEL XT-HS/Low Input kit from Agilent and the UMIs are positioned at index 2 (see picture below  ). The UMIs are in a separate FASTQ...

mosDepth vs plotCoverage

4

--Hi, I encounter differences between the plotCoverage tool and mosdepth (see attachment) and i don't know why. I use the following commands: plotCoverage --bamfiles SRR6823381.bam --BED Exome-Agilent.bed -p max -o...

unable to convert owl format to obo

6

-Hi, last version of robot failed to convert this owl file: https://raw.githubusercontent.com/stemcellontologyresource/OSCI/master/src/ontology/osci.owl is there a specific parameter i need to add ? Thank you. java -jar ./robot.jar convert --input osci.owl...

--hi all, When running strelka step some rares SNVs are not detected and i want to know if there is a way to increase sensitivity, i have tried to set...

CPM output

1

--Hi, is it possible to add an option to output CPM instead of TPM ? thank you --

limitations ?

1

--Hi, program failed with a list of 200000 entries kmer-db build -k 21 -multisample-fasta input.list DGV-kmer-21.db Kmer-db version 1.10.0 (18.07.2022) S. Deorowicz, A. Gudys, M. Dlugosz, M. Kokot, and A....

--Hi, how to change color and type of ablines using ggmaplot, i have tried with: y.ablines.col="blue", y.ablines.linetype="dashed" but nothing change. Thank you --

--Hi all, is ichorCNA able to make analysis on germline samples without control sample (such as CNVkit) ? thank you --

detection of CNV in germlines

1

--Hi, 2 questions: is CONICS able to detect CNV in germlines single cells ? and is there a way to compute mosaicism rate ? thank you --