User: microfuge

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microfuge930
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@microfuge
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Posts by microfuge

<prev • 190 results • page 1 of 19 • next >
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Comment: C: Classify, organize, and cluster a list of proteins / discovering relations betwe
... Simplest would be to put the ids in [string database][1] , presumably if they belong to same species. [1]: https://string-db.org/ ...
written 24 days ago by microfuge930
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Comment: C: DNA Hybridization Melting Temperature Open Source
... How about [EMBOSS suite][1] ? [1]: http://emboss.sourceforge.net/apps/cvs/emboss/apps/dan.html ...
written 4 weeks ago by microfuge930
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Comment: C: Percentage of bases in a fasta sequence
... Definitely not very fast and is ram intensive but this is what I use `grep -v ">" input.fa |grep -o . |sort |uniq -c` Gives counts which can then be converted to percentages ...
written 5 weeks ago by microfuge930
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Comment: C: Software to identify microsatellites, minisatellites and satellites in a plant g
... I have used [Phobos][1] with good results. [1]: http://www.ruhr-uni-bochum.de/ecoevo/cm/cm_phobos.htm ...
written 6 weeks ago by microfuge930
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Comment: C: BigWig from ensembl assembly to UCSC session
... There is a command in ucsc tool kit called bigWigToWig . You can convert bigwig to wig and then use wigToBigWig tool to reconvert ? ...
written 7 weeks ago by microfuge930
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Comment: C: BigWig from ensembl assembly to UCSC session
... chromosome name differences is what first comes to mind. ...
written 7 weeks ago by microfuge930
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Comment: C: GNU parallel error: Command line too long
... Can print the output of ` parallel --max-line-length-allowed` ...
written 9 weeks ago by microfuge930
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Answer: C: Colors UCSC genome browser
... It uses standard [RGB codes][1]. You can Google them to get the code for the color you want (here is first hit: https://www.rapidtables.com/web/color/RGB_Color.html) [1]: https://en.wikipedia.org/wiki/RGB_color_model ...
written 9 weeks ago by microfuge930 • updated 9 weeks ago by zx87544.8k
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Answer: C: Split sequence according the 'N' base
... Another approach based on UCSC utils (http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/) and bedtools . Only suitable for bigger files. - Convert fasta to twobit `faToTwoBit genome.fa genome.2bit` - Get the locations of Ns in bed form `twoBitInfo -nBed genome.2bit N.bed` - Use bedtool ...
written 9 weeks ago by microfuge930
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Answer: C: script for task or AWK
... While the datamash solution is clearly the best, just for fun an attempt based on perl ` perl -MList::Util=min,max -lane 'BEGIN{%y}{$x=@F[0]."\t".$F[1];push @{$y{$x}},@F[-1] }END{foreach(keys %y){my @d=@{$y{$_}};print "$_\t",scalar(@d),"\t",min(@d),"--",max(@d) } }' inputfile.txt ` - seq000002 Fc ...
written 9 weeks ago by microfuge930

Latest awards to microfuge

Scholar 9 weeks 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 9 weeks ago, created an answer with at least 3 up-votes. For A: chain file for maize
Scholar 9 weeks 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 9 weeks ago, created an answer with at least 3 up-votes. For A: chain file for maize
Scholar 10 weeks 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 3 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 5 months ago, created a comment with at least 3 up-votes. For C: Fasta alignment to Tajima's D and population statistics
Popular Question 7 months ago, created a question with more than 1,000 views. For Tissue Specificity index (tau) should FPKM data be log transformed?
Scholar 12 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 12 months ago, created an answer with at least 3 up-votes. For A: chain file for maize
Scholar 13 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 13 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 13 months ago, created an answer with at least 3 up-votes. For A: chain file for maize
Commentator 22 months ago, created a comment with at least 3 up-votes. For C: Fasta alignment to Tajima's D and population statistics
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Teacher 22 months ago, created an answer with at least 3 up-votes. For A: chain file for maize
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Commentator 23 months ago, created a comment with at least 3 up-votes. For C: Fasta alignment to Tajima's D and population statistics
Scholar 23 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

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