User: microfuge

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microfuge710
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@microfuge
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Posts by microfuge

<prev • 162 results • page 1 of 17 • next >
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Comment: C: which one is good mafft or clustalW???
... Page 44 of t-coffee pdf [here][1] provides a detailed comparison. [1]: https://media.readthedocs.org/pdf/tcoffee/latest/tcoffee.pdf ...
written 5 weeks ago by microfuge710
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Comment: C: Finding sample swaps using VCF files
... Hi, One quick way but not for a serious clinical settings is to feed the vcf to vcfkit ([here][1] ) and make a tree out of it. But I don't exactly know the implications for your work. We gave students of our course some paternity testing exercises based on SNPs and they came up with the idea to mak ...
written 5 weeks ago by microfuge710
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Comment: C: Retrieval of similar positions from samples in a vcf but different from referenc
... Would bcftools view work if min alternate allele frequency is set to 1.0 ? bcftools view --min-af 1 input.vcf.gz ...
written 5 weeks ago by microfuge710
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Comment: C: Assumed rate of exonic mutation?
... Not fully sure but the mutation rate should not be less in exons (assuming no DNA composition bias). It is the selection on exons which purges more mutations giving less polymorphism/divergence. Effects of linked selection would also effect synonymous sites decreasing polymorphism and divergence in ...
written 5 weeks ago by microfuge710
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Comment: C: Finding paralogs of gene
... I have used these two and find them to be good http://inparanoid.sbc.su.se/cgi-bin/index.cgi http://eggnogdb.embl.de/#/app/home ...
written 5 weeks ago by microfuge710
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Comment: C: size (how many amino acids) are cytosolic or extracellular in membrane protein
... Would [this][1] be of any use? never used it myself though. [1]: http://embnet.vital-it.ch/software/tmbase/TMBASE_doc.html ...
written 5 weeks ago by microfuge710
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Answer: C: How to print two lines of several files to a new file with the speicific order?
... Just a paste and awk based approach based on the assumption that a) the sequence is in one line and not wrapped b) no tabs spaces in parent fasta. The getline function in awk gets the next line and it is then skipped by awk. paste -d "\t" *.fa |awk '{getline y;split(y,z,"\t");for (i=1;i<=NF ...
written 5 weeks ago by microfuge710
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Comment: C: Reads partly within an exon
... intron retention is not that uncommon in mammals ( http://www.biorxiv.org/content/biorxiv/early/2017/05/09/135624.full.pdf ). In plants quite common in plants (https://www.ncbi.nlm.nih.gov/pubmed/15341630). ...
written 8 weeks ago by microfuge710
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Comment: C: Comparison between multiple fasta files in terms of presence or absence of certa
... I usually like blastclust which is now a legacy software but this post recommending cd-hit might be useful https://www.biostars.org/p/203468/ ...
written 8 weeks ago by microfuge710
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Comment: C: I have a list of 80 ensembl ids(gene stable ids) for which BioMart is not genera
... These ids seem to of the older version of ensemble, if I am not wrong. One way would be to use biomart from archive of old ensemble releases (http://www.ensembl.org/info/website/archives/index.html) ...
written 8 weeks ago by microfuge710

Latest awards to microfuge

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
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: chain file for maize
Scholar 8 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 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
Commentator 11 months ago, created a comment with at least 3 up-votes. For C: Fasta alignment to Tajima's D and population statistics
Supporter 11 months ago, voted at least 25 times.
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: chain file for maize
Centurion 11 months ago, created 100 posts.
Commentator 12 months ago, created a comment with at least 3 up-votes. For C: Fasta alignment to Tajima's D and population statistics
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

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