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Hello Tseemann,
I ran the script "snippy-core --prefix TB0065_S16_L001 TB0207_S6_L001" and I got the following error. Can you help me?
This is snippy-core 4.5.0
Obtained from http://github.com/…
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I'm currently looking at the differences in the read alignments produced by vg and bwa. As the CIGAR strings don’t discriminate between matches and mismatches, I’ve written a Python tool which takes a…
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[14:55:34] Need samtools --version >= 1.7 but you have 0 - please upgrade it.
How to solve this problem, please?
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Hi!
I am trying to use Aquila_stLFR for an animal species. My reference fasta has chromosome names like Scaffold_[number], not chr[number].
Preprocessing was OK, but on step1 I get errors:
``…
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This is possibly related to https://github.com/samtools/htsjdk/issues/1162, but I see issues with BAM too so this is not entirely a CRAM problem. I think it's a generic index related thing, which is …
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Dear all,
I would like to know if there is a way to properly visualize methylation information obtained from modkit in IGV genome browser (testing IGV 2.17 snapshot).
In particular, I ran Dorado wit…
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This is a follow up from the previous issue of #34
Currently when large blocks of sequence are loaded from 'b', we don't have SNPs in this file. I don't know if we need to manually compare it with…
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Encountered problems while solving:
- package samtools-1.6-h3f2fef4_8 requires openssl >=1.1.0,=3.0.2,
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someone can help me? use it to assemble the cholorplast but it gives me that answer,my fasta file was mapped to the whole genome and get with samtools fastq from the bam file ,is it the reason?
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Hi,
I am new to data analysis, we have been doing CnT for histone modifications and transcription factor. First I used the following alignment parameters:
`--local --very-sensitive-local --no-un…