Moderator: h.mon

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h.mon19k
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Posts by h.mon

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Comment: C: Is it ok to use DREME to predict motifs from RNA-Seq data?
... I do not have much experience on motif finding, but for what I've read, DREME is used to predict motifs when there is some reason to believe the data is enriched for some motif, like protein-DNA capture, or protein-RNA. Why would you expect a set of differentially expressed genes to share motifs? ...
written 23 minutes ago by h.mon19k
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Comment: C: Fst and pairwise Fst
... Hi debaratichakraborty31, I reopened your question, but please take some time to improve it. As it stands now, it is poorly formulated and it is unlikely you will get any help. Please read https://www.biostars.org/p/75548/ for hints. ...
written 1 hour ago by h.mon19k
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Comment: C: Fst and pairwise Fst
... Hello debaratichakraborty31! We believe that this post does not fit the main topic of this site. Not a bioinformatics question (What is the difference between Fst and pairwise Fst?) and not enough information provided (How to calculate it in GenoDive?). For this reason we have closed your questi ...
written 2 hours ago by h.mon19k
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Comment: A: PSMC: fq2psmc conversion problems
... PSMC is intended to infer population history from **one** diploid genome. Have a look at [MSMC][1]. [1]: https://github.com/stschiff/msmc ...
written 3 hours ago by h.mon19k
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Comment: C: Mauve Contig Mover
... The image linked has no screenshot of folder. Besides, **don't send a screenshot of a folder**, list its contents as text. ...
written 3 hours ago by h.mon19k
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Answer: A: Use OrthoDB to retrieve the orthologs between human and bacteria
... You are correct, OrthoDB restricts orthologs by clade: > There are 290 orthology levels, that were retrieved from the NCBI Taxonomy (12): 116 eukaryotes (one for plants, 54 for animals, 60 for fungi), 136 for bacteria, 22 for archaea and 16 for viruses. Quoted from the paper [OrthoDB v9.1: cata ...
written 13 hours ago by h.mon19k
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Answer: A: Proper design for DESeq2 and other RNAseq general questions
... From the description of your experiment, I think your design should be only `tissue`, why are you including `tissue*tree`? Having two replicates for pollen is not ideal, but shouldn't cause errors. > Also, I am concerned that my counts are not normalized well-enough by calculating FPKM values. M ...
written 14 hours ago by h.mon19k
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Comment: C: EMBOSS transeq translate to protein with 3 letter code
... Not quite right, the general pattern is you have to insert one initial space, then two spaces between every amino acid, then a final space. There are several tricks around to split a string into characters. As I like perl, `split //, $_` would split a string at every character, then join with `join` ...
written 16 hours ago by h.mon19k
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Comment: C: Get CDS from consensus genome assembly
... > The reference-genome assemblies were obtained wit: GATK, samtools mpileup, bcftools, vcfutils.pl and seqtk. This really doesn't explain what you have done. I suspect you have several resequencing genomes, by the list of tools used. And you suspect some of these genomes will have additional gen ...
written 16 hours ago by h.mon19k
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Answer: A: Trimmomatic execution removes the data from my fastq sequence file. What am I do
... You have to pass the full path to both R1 and R2 files, not just for the R1 file as you are doing. Also, I don't know if the rest of your command is correct, as I don't use Trimmomatic, but I believe it isn't, as the manual states it needs either a `--baseout` parameter, or 4 file names for output f ...
written 19 hours ago by h.mon19k

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Appreciated 1 day ago, created a post with more than 5 votes. For Where did EMBOSS go?
Commentator 2 days ago, created a comment with at least 3 up-votes. For C: STAR align multiple files
Teacher 3 days ago, created an answer with at least 3 up-votes. For A: What might explain the "[blastall] ERROR: Arguments must start with '-'" error i
Teacher 3 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
Scholar 3 days ago, created an answer that has been accepted. For A: Extract fasta sequences from a large file using a list of names
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Teacher 5 days ago, created an answer with at least 3 up-votes. For C: Identify insertions with IGV
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