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Hello! I am trying to run svaba for targeted SV detection.
The command works with Svaba v1.1.0 but with v1.2.0 it throws the following error:
```
"Found chromosome in region file /rtsess01/juno/…
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In many whole genome _de novo_ sequencing project, the scaffolds and contigs are not assembled into pseudomolecules. As a result, it's very difficult to determine exact ratio between subject genome an…
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I input an unpublished reference assembly to stringtie with the -G option . The reference gtf has no UTR data; the transcript boundaries in every case are coterminous with the 5' and 3' coordinates of…
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Hi, @eblerjana
I found that several samples's peak is wrong according the pangenie log. So would you mind teliing what's the influence of these peak? Is there any way to set peak?
Here is a ex…
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### Description of bug
I am trying to assemble several low coverage spider genomes (2X-10X) with Spades using the following command:
spades.py -1 ../File_1_paired.fq.gz -2 ../File_2_paired.fq.gz -t …
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Hi Ben,
The "contig" mode doesn't provide "relative_abundance" option for coverage measures. Could you please explain the reasons for this setting? What are your concerns about calculating the rela…
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Hi! Francisco
While running the `-t abundance ` I am running into a problem with the sam to bam conversation due to a duplicate header. When I checked the grep "NODE_1753_length_683_cov_1.602310" FDS…
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Hi,
I'm running variant calling on non-model organisms, and for some of the downstream analyses (e.g., nucleotide diversity calculations), it is necessary to generate (possibly boolean) accessibili…
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Hello dear developers,
I am using PECAT to assemble a diploid genome (SMRT Cell, PacBio), however, the process is stuck at the assembly stage, the following error appears:
```
2024-07-31 11:0…
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I am trying to use findZX on reads that have already been trimmed, but I keep getting an error that only happens when I skip the trimming part of the pipeline.
Is there a way around this? Or should…