User: microfuge

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microfuge900
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Posts by microfuge

<prev • 184 results • page 1 of 19 • next >
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Comment: C: GNU parallel error: Command line too long
... Can print the output of ` parallel --max-line-length-allowed` ...
written 5 days ago by microfuge900
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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 6 days ago by microfuge900 • updated 6 days ago by zx87544.5k
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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 6 days ago by microfuge900
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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 "$_\t",scalar(@d),"\t",min(@d),"--",max(@d) } }' inputfile.txt ` - seq000002 Fc ...
written 7 days ago by microfuge900
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Comment: C: Faster alternative of NCBI eutils
... Sorry my bad. You need to choose send to -> file option and then select Summary (Text). The web page by default displays only 20 entries. ...
written 11 days ago by microfuge900
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Comment: C: Faster alternative of NCBI eutils
... Not a programatic approach but you can use batch entrez (https://www.ncbi.nlm.nih.gov/sites/batchentrez) Batch Entrez -> Select Data base BioSample -> Upload biosample id list -> Retrieve Records -> Select summary Text -> Download The file -> Grep "^Identifiers" ...
written 11 days ago by microfuge900
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Comment: C: how to analyze synteny between 4 genomes. please suggest suitable tool
... Synmap is a good tool but works only up to 3 genomes (https://genomevolution.org/coge/SynMap3D.pl) ...
written 14 days ago by microfuge900
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Answer: C: Mimic input file with string
... Would this work ? ` bedtools getfasta -fi genome.fa -bed <(echo chr1$'\t'5$'\t'10)` ...
written 14 days ago by microfuge900
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Comment: C: Finding restriction sites when the gene is on the negative strand
... I am also often confused. The best way for me is to use UCSC genome browser and its Restr_enzyme track. You can try UCSC genome browser-> human -> hg19 and then click hide all. Then add custom track and paste `chr11 355953 356144 TestGene 1000 + ` Then in mapping and sequencing click on rest ...
written 27 days ago by microfuge900
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Answer: C: Recreate reference fasta from bam file
... Although reassembly seems the preferred option I thought if Pilon which polishes a reference with standard illumina reads could work . Just for fun I tried following with an ecoli MG1655 bam file. - Got the length and name of reference chromosome from bam header (in this case only one) - Creat ...
written 5 weeks ago by microfuge900 • updated 5 weeks ago by genomax49k

Latest awards to microfuge

Teacher 6 days ago, created an answer with at least 3 up-votes. For A: chain file for maize
Teacher 7 days ago, created an answer with at least 3 up-votes. For A: chain file for maize
Scholar 14 days 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 5 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
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: Fasta alignment to Tajima's D and population statistics
Popular Question 5 months ago, created a question with more than 1,000 views. For Tissue Specificity index (tau) should FPKM data be log transformed?
Scholar 10 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 10 months ago, created an answer with at least 3 up-votes. For A: chain file for maize
Scholar 11 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 11 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 11 months ago, created an answer with at least 3 up-votes. For A: chain file for maize
Commentator 20 months ago, created a comment with at least 3 up-votes. For C: Fasta alignment to Tajima's D and population statistics
Supporter 20 months ago, voted at least 25 times.
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: chain file for maize
Centurion 20 months ago, created 100 posts.
Commentator 21 months ago, created a comment with at least 3 up-votes. For C: Fasta alignment to Tajima's D and population statistics
Scholar 21 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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