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Hi, I tried rsem-calculate-expression using bowtie, and the mapping step appeared to be completed. Then I got the error message
"The SAM/BAM file declares less than one reference sequence!"
sin…
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## Expected Behavior
easy-search should finish execution without errors
## Current Behavior
Error during pre-filter step
> Index table k-mer threshold: 0 at k-mer size 15
> Index table: …
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```
What steps will reproduce the problem?
1. prank -d=EOG78Q418.fa -o=EOG78Q418
2. Same problem whether using prank compiled from source or pre-made binary
3. prank works well for the vast majority o…
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Hello!
When it comes to structural variant calling, one characteristic of the presence thereof is a noisier sequence than usual. With these noisy sequences, the secondary alignment can then provide…
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Hi Felix,
I have a couple of questions regarding Bismark. I'm sorry if they are stupid questions; I am fairly new to WGBS data and Bismark analysis (or to bioinformatics in general).
We are rese…
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Hi,
I'm really interested in using graphmap for doing some Nanopore alignments with predicted sequences but I can not seem to get an alignment. I tried to get an alignment with a simple sequence ju…
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Hi there,Do I need full-length transcripts to use ESPRESSO? For example, if the reads are not full-length, do they need to be filtered out?
Why do different positions of the same transcript support d…
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I want to only use the genetic distance from inputted sequence alignments to get the cut-off values, is that possible?
BTW, if construct trees, can I use other softwares, like fasttree, phyml, raxml?
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Frameshift aignments are very useful for Nanopore data, where indels are common. It can also be used for virus-related research, as [some phages have conversed programmed frameshifts](https://www.cell…
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Hi,
I am using the recomputed_alignments_mmseqs.py to search for MSA for my input.fasta which has 9 sequences inside.
but the mmseq2 is taking too long to run it, it is already over 4 hours, but st…