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Hello,
I have an issue while running MANTIS on exome datasets.
I wrote the following code lines :
`python2.7 mantis.py -b ../../Test_MANTIS/genome_scan.bed --genome ../../Test_MSISensor/Indexe…
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I read the CENTIPEDE manuscript. I think the author scanned all putative TFBS across the genome.
However, in your tutorial, you suggested using FIMO only to obtain TFBS in peak regions.
Is it pr…
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Hiya,
Me again. I've realigned my sequences to the reference genome so they are in order and re-ran, which appeared successful until I got these errors:
Error in log10(ldrollsub$compldfisub) …
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Hi,
I am trying to assemble three plant mitochondrial genome sequences using Novoplasty. I successfully assembled two mitochondrial genomes. But When I try to assemble the third genome sequence usi…
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**Motivation**: There are many steps within _breseq_ that could be easily parallelized to speed up execution.
**Implementation**: Use a thread pool that relies only on C++11 std:thread to maximize …
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Hi!
I am using Hmmer3 with bivalve genomes looking for 70-80 aa genes. BUSCO scores for the genomes are in the upper 90s (96-98% complete for BUSCO Metazoa) and most assemblies are chromosome-scale…
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Hello
I try to run barrnap to identify rRNA from a eukaryotic genome , the commad as follow:
barrnap --kingdom euk --threads 20 --outseq rRNA.fasta < chr1.fasta
After running, we got followin…
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I'm running the selection scan in PCANGSD and getting really high pvalues. I've tried numerous options, but always end up with results like what I've attached here. Might anyone have any thoughts on…
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Potential enhancements of Snippy Streamline to be discussed:
- Quality assessment of reference genome (N50, number of contigs, BUSCO) added to Terra outputs
- additional output column that indicat…
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For many circular genomes, gene annotations in NCBI RefSeq overlap the "end" of the linear representation, i.e. the arbitrary nucleotide chosen to be "position 0" for the linear representation of the …