User: microfuge

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microfuge1.5k
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Posts by microfuge

<prev • 252 results • page 1 of 26 • next >
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Comment: C: Obtain N50 stats from NCBI for all Hymenoptera genome assemblies
... Really liked this solution! ...
written 11 days ago by microfuge1.5k
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Comment: C: how can i find all of genes involve in special disease?
... If genes are from a particular species only this can be done with biomart * Go to ensembl biomart https://www.ensembl.org/biomart/martview/31624ea7ad77f20bf544e31b22268447 * Select human genes * In Filters tab on the left side expand phenotype tab * Scroll down the list to get to phenotype/disea ...
written 12 days ago by microfuge1.5k
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Comment: C: How to calculate GC% at 1st, 2nd and 3rd codon position for each sequence in a m
... A blast from the past but codonw calculates per sequence GC3 and many other stats directly from the CDS fasta file http://codonw.sourceforge.net/#Downloading%20and%20Installation . ...
written 12 days ago by microfuge1.5k
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Comment: C: Obtain N50 stats from NCBI for all Hymenoptera genome assemblies
... I always find convinient to start with NCBI Taxonomy. One approach can be - - In NCBI taxonomy https://www.ncbi.nlm.nih.gov/taxonomy enter Hymenoptera in search box - Click on resulting link which opens this page https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=7399 - Check the Genome ...
written 12 days ago by microfuge1.5k
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Comment: C: Is there a database with calculated Ka/Ks ratios for human/mouse genomes?
... It does provides ka/ks values in Attribute -> Homologous (radio button) -> Orthologs -> scroll down to locate species (mouse) -> radio buttons (dn with mouse and ds with mouse) ...
written 13 days ago by microfuge1.5k
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Answer: C: Is there a database with calculated Ka/Ks ratios for human/mouse genomes?
... Ensembl biomart proivides the list. https://www.ensembl.org/info/data/biomart/index.html ...
written 13 days ago by microfuge1.5k
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Answer: C: Align to a single gene -- best procedure
... I would strongly be for aligning to whole genome and not to a specific gene (unless it was targeted sequencing and not WGS). In absence of a complete reference the aligner would force reads from other regions on to partial reference. ...
written 29 days ago by microfuge1.5k
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Comment: C: gff3 header delimiter space or a tab
... Thanks so much! This was a fake gff entry I created, just wanted to know if the official specification says something about it. Did not know about the set list option in vi (quite nice :) ). ...
written 4 weeks ago by microfuge1.5k
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gff3 header delimiter space or a tab
... Dear All, I could not find a source which states the field delimiter to be used in gff3 header. Can it be a space or a tab or it should be a space only ? My hunch is a space. ##gff-version 3 ##sequence-region 1 10 Many Thanks! ...
gff3 written 4 weeks ago by microfuge1.5k • updated 4 weeks ago by Carambakaracho1.9k
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Comment: C: Watterson's theta per site
... I used a perl script to convert did not know that Tassel can do that ( Here seems to give some other ways as well https://www.biostars.org/p/356062/ ) ...
written 8 weeks ago by microfuge1.5k

Latest awards to microfuge

Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: chain file for maize
Voter 3 months ago, voted more than 100 times.
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: Fasta alignment to Tajima's D and population statistics
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: Fasta alignment to Tajima's D and population statistics
Scholar 9 months ago, created an answer that has been accepted. For C: BedTools getfasta -split
Guru 9 months ago, received more than 100 upvotes.
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: chain file for maize
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: chain file for maize
Scholar 18 months ago, created an answer that has been accepted. For A: Many SRR files for one experiment. What are the steps to be taken before further
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: chain file for maize
Scholar 18 months ago, created an answer that has been accepted. For A: Many SRR files for one experiment. What are the steps to be taken before further
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: chain file for maize
Scholar 18 months ago, created an answer that has been accepted. For A: Many SRR files for one experiment. What are the steps to be taken before further
Scholar 19 months ago, created an answer that has been accepted. For A: Many SRR files for one experiment. What are the steps to be taken before further
Commentator 20 months ago, created a comment with at least 3 up-votes. For C: Fasta alignment to Tajima's D and population statistics
Popular Question 23 months ago, created a question with more than 1,000 views. For Tissue Specificity index (tau) should FPKM data be log transformed?
Scholar 2.3 years ago, created an answer that has been accepted. For A: Many SRR files for one experiment. What are the steps to be taken before further
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: chain file for maize
Scholar 2.4 years ago, created an answer that has been accepted. For A: Many SRR files for one experiment. What are the steps to be taken before further
Scholar 2.4 years ago, created an answer that has been accepted. For A: Many SRR files for one experiment. What are the steps to be taken before further
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: chain file for maize
Commentator 3.1 years ago, created a comment with at least 3 up-votes. For C: Fasta alignment to Tajima's D and population statistics
Supporter 3.2 years ago, voted at least 25 times.
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: chain file for maize
Centurion 3.2 years ago, created 100 posts.

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