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# To Do
- [x] Literature review of spliced short read alignment methods (is anyone using Minimap2?)
- [x] Review Rust libraries for alignment and minimizers
- [x] Make stand-alone command line Ru…
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Number of reads generated by some of the tools managed by `rnftools` is not precisely as requested, presumably due to a read being output based on some probability calculation, taking into considerat…
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**Version info**
- bcbio version (`bcbio_nextgen.py --version`): v1.2.9
- OS name and version (`lsb_release -ds`): Red Hat Enterprise Linux release 8.5 (Ootpa)
**To Reproduce**
Exact bcbio comma…
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When I run **BAMboozle 0.5.0** on BAM files generated with **Salmon 1.6.0**, I get the following error message:
```
BAMboozle --bam sample01.bam --out sample01.anonym.bam --fa /mnt/data/reference_…
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Currently, progressiveCactus requires a long time to run ( 120 * (n-1) CPU days for n genomes, from another thread here) and therefore requires leveraging a cluster, which we cannot do at my instituti…
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Hi,
I am trying to run star-fusion with the command:
```
STAR-Fusion \
--genome_lib_dir /fdb/CTAT/__genome_libs_StarFv1.10/GRCh37_gencode_v19_CTAT_lib_Mar012021/ctat_genome_lib_build_dir/ …
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Hi, there.
I'm user of Isaac aligner and isaac variant caller.
I realigned Hiseq reads by Isaac aligner and then called variant by isaac variant caller with following commands.
isaac-align -r /path t…
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Dear All,
I am using STAR aligner to map the Paired RNA seq reads to genome data using the below scripts:
./STAR --runMode alignReads --runThreadN 16 --genomeDir /home/taiwo/star/STAR-2.5.3a/bin/L…
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This is related to #232 I was getting on my laptop - the `"Bio.Alphabet has been removed from Biopython` error. You had suggested trying version `2.2.8` so I'm pulling the latest master from github to…
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Hi Adam,
I got an empty bam file after addsnv.py. The command is :
`addsnv.py --varfile simu_snv_sites.txt --bamfile simu_N.bam --reference ucsc.hg19.fasta --procs 12 --maxdepth 4000 --cover…