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Hello,
I have some CAGE sequencing data from oil palm. The reads were mapped to the genome. I have alignment BAM file, and converted into BigWig. I have problem running quantifyCTSSs because I couldn…
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I have an alignment of 58 snake genomes stored as a HAL file and generated using Progressive Cactus. For each genome in the alignment, I have a BED file specifying site positions in the ungapped genom…
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I have 5 mammalian genomes that I am trying to align using progressiveCactus.
When I try to run all 5, it takes months on my limited available computational resources.
However, I managed to run 2 of…
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Dear
I met with such error:
[Fri Sep 20 17:27:52 2024] Enqueueing pair 2238009/2240249 (99.9%). Est. time left: 00:00:34 (hh:mm:ss)
[Fri Sep 20 17:28:47 2024] 2240249/2240249 (100%) pairs align…
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Hello,
I run bamquery
```python
!python xxx/Software/bamquery/BamQuery/BamQuery.py xxx/Software/bamquery/BamQuery try_1 v38_104 --mode normal --t 8 --plots
```
And my output is as follows,
`…
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I have been trying to use decoil installed from source but I am experiencing an Error. Example command:
```
for SAMPLE in 1 2 3 4
do
mkdir -p ${SAMPLE}T/logs
mkdir -p ${SAMPLE}T/tmp
export B…
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Hi, this project looks good! Thanks!
I would like to use Tark as a source of transcripts for [Biocommons HGVS Python library](https://github.com/biocommons/hgvs)
RefSeq transcripts can differ fr…
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Hi,
I use vclust script to classify viruses into species and genera following ICTV standards.
The script of assigning viruses into putative species (tANI ≥ 95%) is:
`vclust cluster -i ani.tsv -o …
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Hi,
I have a question regarding running LASTZ similar to what they did for the TOGA paper. In my case, I have Cactus 447 mammalian genome dataset. I converted it from Hal to fasta, removed ancestral …
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Hello,
I am using TEcount to calculate the expression levels of TEs in Macaca. The genome and annotation files were downloaded from NCBI, and the TE annotation file was obtained from your website. …