Moderator: h.mon

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h.mon31k
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Posts by h.mon

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Comment: C: There is a convenient way to use not up-to-date packages in R?
... Old versions of Windows R here: https://cran.r-project.org/bin/windows/base/old/ If you want the 2.13 version of the BioConductor package, you will need R 3.0.2, see [here][1]. [1]: https://bioconductor.org/news/bioc_2_13_release/ ...
written 6 hours ago by h.mon31k
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Comment: C: RNA-Seq by Example book: Installing DESeq2 using libopenblas==0.3.7 is not wokin
... See this page: [Biostar Handbook Issues][1]. Before opening an issue, be sure if the same issue hasn't been reported before. If you do find the issue is new, please provide more details, such as error messages - there are many ways something may "not work". [1]: https://github.com/biostars/biosta ...
written 17 hours ago by h.mon31k
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Answer: A: Error installing MITE-Hunter
... You can still download and install the latest version of legacy BLAST from here: https://ftp.ncbi.nlm.nih.gov/blast/executables/legacy.NOTSUPPORTED/2.2.26/ Note the very subtle **NOTSUPPORTED** in the ftp path. As MITE-Hunter and the BLAST version it depends on are old and unsupported, maybe you s ...
written 18 hours ago by h.mon31k
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Comment: C: From accession ID to phylum taxid
... The fastest way would be to download the base files from NCBI and parse the information you need from them. This is the approach taken by several tools that need to gather taxonomic information from NCBI accessions, such as [BlobTools][1] or [KronaTools][2]. [1]: https://github.com/DRL/blobtool ...
written 1 day ago by h.mon31k
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Comment: C: I have aligned reads and gene counts from STAR. How should I calculate TPM from
... If you have the genome and a gtf annotation, you can extract the transcriptome with a number of different tools, such as [gffread][1]. RSEM also need a transcriptome fasta, so you would have the same problem - although RSEM also provides an script to extract the transcriptome fasta from a genome fas ...
written 1 day ago by h.mon31k
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Answer: A: Use PCoA plot rather than phylogenetic tree?
... As long as you can calculate a distance / similarity matrix between the sequences, you can then use this matrix in a number of visualization methods, such as PCA, PCoA, etc. The question is why you would do that? Relationship between sequences is best viewed and interpreted as a phylogenetic tree, ...
written 1 day ago by h.mon31k
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Answer: A: Program to plot 60,000 16S rRNA dataset for phylogenetic assessment?
... Beta-diversity is a ratio between regional and local species diversity (abundance), and a PCA plot would depict the distances in some estimate of beta-diversity between the amostral units. Therefore, you can't include individual sequences in a PCA plot depicting beta-diversity, because individual se ...
written 1 day ago by h.mon31k
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Answer: A: I have aligned reads and gene counts from STAR. How should I calculate TPM from
... You can use [Salmon][1] to estimate transcript counts and TPMs using the **Aligned.toTranscriptome.out.bam**. The result would be similar to RSEM, but it would run much faster. If you estimate TPMs with Salmon, be consistent and also use the counts estimated by Salmon, instead of the STAR counts. Y ...
written 1 day ago by h.mon31k
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Answer: A: Try to find a tool for creating a pipeline with PBS scripts?
... It is possible to use make with PBS, one just needs some creativity - see [gnu-make-job-scheduler][1]. But you probably want a workflow manager such as CWL, Nextflow or Snakemake - there are many others, but I think those are the "most famous". [1]: https://github.com/inodb/gnu-make-job-schedule ...
written 3 days ago by h.mon31k
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Comment: C: How to get transcripts lengths from RNAseq data to calculate TPM
... The raw counts correspond to gene expression estimates or transcript expression estimates? ...
written 6 days ago by h.mon31k

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Scholar 19 days ago, created an answer that has been accepted. For A: Script for extracting data from a tab-delimited file
Teacher 21 days ago, created an answer with at least 3 up-votes. For A: Hi blog how to calculate differntial expression analysis if thre is no replicate
Teacher 22 days ago, created an answer with at least 3 up-votes. For A: Hi blog how to calculate differntial expression analysis if thre is no replicate
Good Answer 23 days ago, created an answer that was upvoted at least 5 times. For A: How to build a local Pfam database?
Teacher 24 days ago, created an answer with at least 3 up-votes. For A: Hi blog how to calculate differntial expression analysis if thre is no replicate
Good Answer 24 days ago, created an answer that was upvoted at least 5 times. For A: How to build a local Pfam database?
Appreciated 24 days ago, created a post with more than 5 votes. For A: Metagenomic Data management
Teacher 27 days ago, created an answer with at least 3 up-votes. For A: Hi blog how to calculate differntial expression analysis if thre is no replicate
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Commentator 4 weeks ago, created a comment with at least 3 up-votes. For C: RCurl instalation problem
Commentator 4 weeks ago, created a comment with at least 3 up-votes. For C: RCurl instalation problem
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Hi blog how to calculate differntial expression analysis if thre is no replicate
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Hi blog how to calculate differntial expression analysis if thre is no replicate
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Hi blog how to calculate differntial expression analysis if thre is no replicate
Good Answer 4 weeks ago, created an answer that was upvoted at least 5 times. For A: How to build a local Pfam database?
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Hi blog how to calculate differntial expression analysis if thre is no replicate
Good Answer 5 weeks ago, created an answer that was upvoted at least 5 times. For A: Are all RPKM/FPKMs in RNAseq "equal" ?
Appreciated 7 weeks ago, created a post with more than 5 votes. For Technical Or Biological Replicate
Scholar 7 weeks ago, created an answer that has been accepted. For A: Script for extracting data from a tab-delimited file
Scholar 7 weeks ago, created an answer that has been accepted. For A: Script for extracting data from a tab-delimited file
Appreciated 8 weeks ago, created a post with more than 5 votes. For Benchmarking bioinformatics tools
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: Hi blog how to calculate differntial expression analysis if thre is no replicate
Scholar 8 weeks ago, created an answer that has been accepted. For A: Script for extracting data from a tab-delimited file
Scholar 8 weeks ago, created an answer that has been accepted. For A: Script for extracting data from a tab-delimited file
Good Answer 8 weeks ago, created an answer that was upvoted at least 5 times. For A: Are all RPKM/FPKMs in RNAseq "equal" ?

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