speedseq
speedseq copied to clipboard
hall-lab
A flexible framework for rapid genome analysis and interpretation
Hi, I just want to ask whether Linux/Mac ARM64 is supported ? Thank you!
Hello, I am trying to get somatic mutations from `speedseq somatic` but it has been more than 24 hours but it is still running and no output is generated. Here...
I am trying to get somatic mutations using speedseq somatic function. But everytime I am getting an error of mismatch line length. I am using hg19 fasta file from UCSC....
Hi I Used this command: speedseq align \ > -o 5863-DD-3 \ > -R "@RG\tID:5863-DD-3\tSM:5863-DD-3\tLB:ILLUMINA" \ > assembly38.fasta \ > 5863-DD-3-R1_001.fastq.gz \ > 5863-DD-3-R2_001.fastq.gz I have the discordant and splitters...
I am trying to install the speedseq using: `git clone --recursive https://github.com/hall-lab/speedseq` However, when I use `make` I get this error message: /usr/include/c++/8/bits/stl_tree.h:777:8: error: static assertion failed: comparison object must...
Thanks a lot for developing this pipeline. I have a question about BWA MEM alignment. In your [main paper](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4589466/) you mention that: `SpeedSeq aligns paired-end FASTQ files to the human...
Hi folks, Is there a docker or singularity container available for me to run speedseq sv? thanks, Richard
Dear Group, I am trying to install SpeedSeq with cnvnator. A `make cnvnator` produces a linker error when trying to link in ROOT. I have tested the link command with...
Link to parallel @ 8a570f8 in src/ is dead, which prevents speedseq from building. Trying to use git clone git://git.savannah.gnu.org/parallel.git as suggested in #124 hangs. Trying to access git://git.savannah.gnu.org/parallel.git or...
Is it possible to run speedseq var and sv only on specified genomic regions? we are interested in looking at variations only in certain regions of interest and being able...
