Moderator: h.mon

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h.mon28k
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Posts by h.mon

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Answer: A: Converting an output de-novo transcriptome assembled with Trinity to a .gff3 fil
... featureCounts assigns zero counts to multi-mapped reads. Trinity assemblies have a lot of "redundancy", as the assembler tries to recover all possible isoforms of a gene. This would mean a lot of the mapped reads would map to multiple locations (to several isoformrs), and featureCounts would assign ...
written 2 hours ago by h.mon28k
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Comment: C: running RAxML and MrBayes over concatinated multiple sequence alignments
... Both IQ-TREE and FastTree are faster than RAxML, by 10-50x. RAxML has been superseded by RAxML-NG, which is supposedly faster, by I haven't seen benchmarks. I am not up-to-date regarding Bayesian phylogeny software, but I think BayesAss is faster than MrBayes. ...
written 3 hours ago by h.mon28k
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Comment: C: running RAxML and MrBayes over concatinated multiple sequence alignments
... Yes, the partitions file is assigned with `-q`. ...
written 5 hours ago by h.mon28k
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Comment: C: index genome using haploid genome.fa or diploid genome.fa?
... See these previous discussions: https://www.biostars.org/p/259224/ https://www.biostars.org/p/305531/ https://www.biostars.org/p/311061/ ...
written 5 hours ago by h.mon28k
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Comment: C: running RAxML and MrBayes over concatinated multiple sequence alignments
... The script [BeforePhylo][1] can concatenate the alignments and create the RAxML partition table for you. [1]: https://github.com/qiyunzhu/BeforePhylo ...
written 5 hours ago by h.mon28k
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Answer: A: calculating consensus tree phylogeny
... You want to look at supertree methods. e.g., [A supertree pipeline for summarizing phylogenetic and taxonomic information for millions of species][1]. [1]: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5335690/ ...
written 5 hours ago by h.mon28k
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Comment: C: Is there any tool available for sequence alignment concatenation and supermatrix
... How did you end up with different length sequences? MAFFT should add `-` to pad all alignments to the same length, and then Gblocks only remove columns, so all sequences should still have the same length. If the sequences do not have the same length, they may be improperly aligned, I would suggest y ...
written 5 hours ago by h.mon28k
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Comment: C: Is there any tool available for sequence alignment concatenation and supermatrix
... I would suggest you to check if all sequences have the same length at the file **gene1.fasta**, and fix their lengths if they differ. ...
written 7 hours ago by h.mon28k
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Answer: A: rRNA and bacteria: Absence and duplicates
... > the copies of 23SrRNA are identical to each other and the copies of 16SrRNA are identical to each other. I wanted to ask if this seems feasible that a bacteria sample should have exactly the same rRNA repeated in such manner Yes: [Multiple Ribosomal RNA Operons in Bacteria; Their Concerted Evo ...
written 7 hours ago by h.mon28k
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Comment: C: ORF finder v0.4.1
... The changelog since ORFfinder 0.4.1 doesn't suggest any ground-breaking changes: 02/26/2017 - v 0.4.3 Built with statically linked libstdc++ (on issue of GCC-4.9 libraries not yet supported on CentOS7) 02/13/2017 - v 0.4.2 For file input with multiple FASTA sequen ...
written 7 hours ago by h.mon28k

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Scholar 7 days ago, created an answer that has been accepted. For A: Error in installation of RandFold 2.0
Scholar 11 days ago, created an answer that has been accepted. For A: Error in installation of RandFold 2.0
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Teacher 28 days ago, created an answer with at least 3 up-votes. For A: Are all RPKM/FPKMs in RNAseq "equal" ?
Teacher 28 days ago, created an answer with at least 3 up-votes. For A: What are "HET" regions in a genome?
Scholar 28 days ago, created an answer that has been accepted. For A: Error in installation of RandFold 2.0
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Scholar 6 weeks ago, created an answer that has been accepted. For A: What are "HET" regions in a genome?
Good Answer 7 weeks ago, created an answer that was upvoted at least 5 times. For A: Are all RPKM/FPKMs in RNAseq "equal" ?
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: What are "HET" regions in a genome?
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Scholar 11 weeks ago, created an answer that has been accepted. For A: What are "HET" regions in a genome?
Scholar 11 weeks ago, created an answer that has been accepted. For A: What are "HET" regions in a genome?

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