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From this call:
```
addSpacerAlignments(guideSet,
aligner="bowtie",
aligner_index=canFam3,
bsgenome=BSgenome.Cfamiliaris.UCSC.canFam3,
n_mismatches=3,…
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Dear Developer
I am using 'redundant' running my assemble genome.
I am using different parameters running twice, including reduce the cover identity value.
The survey shows this species genome ha…
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Dear Crispresso team,
We happened to have a mixed sample of insertion libraries which differ just by 3 bp of the insertion. I was wondering if in your experience CrispressoPooled can be used in thi…
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Hi all,
I have set up the nextflow locally on my server. I have an error on making the genome size file by samtools as below:
Error executing process > 'NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:CUSTOM_GE…
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I run it as
`bismark_genome_preparation --path_to_aligner --bowtie2 --verbose --large-index --parallel 4`
on a Macbook Pro with 10 cores. However, it runs over a single thread. I also run with d…
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Dear teacher, thank you for the excellent tools provided！
I am using it for my non-model plants, and I have the complete reference genome and gtf annotation files.
So i run it with -genome and -g…
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I am trying to align queries that sometimes have large gaps (e.g., several hundred nucleotides) relative to the target. These are not due to splicing, they're due to deletions in the query relative to…
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scTE fails to find cell barcode information in bam files I generated using the cell ranger pipeline:
```
$ scTE -i possorted_genome_bam.bam -o out_rep2 -x /software/scTE/mm10.exclusive.idx --hdf…
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Hi Manish,
I have a few questions regarding getting the whole genome alignments of two set of plant genomes. My understanding is that nucmer is generally more sensitive while that is not the case w…
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### Description of the bug
Hello,
I am testing the alevin-fry branch and came across this error message at the indexing step:
`Error: pyroe failed to return succesfully ExitStatus(unix_wait_status(…