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### Instructions
it‘s my first time to run the pipline for RNA-seq data.
the log of SplitNCigarReads makes me confused which said '00:39:03.278 WARN IntelInflater - Zero Bytes Written : 0' at belo…
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I did a fresh install of flye with micromamba. Python is 3.9.
I get a core dump on the minimap2 step. Any suggestions?
Thanks!
less /Spawn/Isolates/LT001001/results_flye_correct/10-consensu…
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The current samtools view behavior is to extract any read that overlaps with the target region, I wonder if it is possible to add an option to select only reads whose start coordinates fall inside the…
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I'm unable to get pysam to work with google storage urls, here's what I'm doing:
export HTSLIB_CONFIGURE_OPTIONS="--enable-plugins --enable-libcurl --enable-gcs"
pip3 install -v --no-use-wheels py…
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Hi folks,
I'm trying cudamapper with this command:
`/opt/GenomeWorks-2021.02.2/bin/cudamapper PAG33026_pass_concat.fastq.gz ../hg19a.fa -B > cudamapper_2021_02_02_GM24385.bam`
which outputs quite…
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Hello!
There is an error when I apply GangSTR on 3079 samples, I am informed that there are no enough reads for some samples and I don’t know how to set insert size distribution manually.
I attempt…
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Dear Alaina,
I've been trying to set up the latest version of liftoff in a MacBook (M1) and a linux-based HPC following all your instructions. Both conda and pip liftoff installation fail.
### c…
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We could use a more descriptive error, here.
We run into this …
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This is similar to issue #107.
We would like an interface where one can specify chromosome + region, and obtains only the parts of the VCF that correspond to this query. This would most likely mean…
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If we are ever going to have a "performance mode", we need to know what areas need compiler switches for performance. This could be done either by benchmarking or by simple algorithmic analysis (eyeba…