User: microfuge

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microfuge610
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Posts by microfuge

<prev • 155 results • page 1 of 16 • next >
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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 3 days ago by microfuge610
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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 3 days ago by microfuge610
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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 4 days ago by microfuge610
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Comment: C: Bedtools intersect QTL animalgenome
... Just an observation from the bedtools source if (len < 1 || len > 10) { fprintf(stderr, "***** ERROR: too many digits/characters for integer conversion in string %s. Exiting...\n", str); exit(1); } The coordinates seem to be under 10 digits. I could get get the error after giving a ...
written 7 days ago by microfuge610
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Comment: C: Determining the correct reading frames for transcripts for dn/ds calculation
... It is typical to take the longest ORF. But [here][1] is a relevant study. [1]: https://academic.oup.com/gbe/article/5/2/457/562605/Improving-Genome-Wide-Scans-of-Positive-Selection ...
written 7 days ago by microfuge610
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Answer: C: Bacterial Type strain and Proxytype strain in NCBI
... Seems so from the file link in your post. The last column (relation_to_type_material) has following possible entries- **relation_to_type_material** - assembly from proxytype material - assembly from synonym type material - assembly from type material ...
written 8 days ago by microfuge610
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Comment: C: bedtools closest gives a -1 distance with -io (ignore overlaps)
... Could this be the reason ?. Help message output from bedtools closest - Notes: Reports "none" for chrom and "-1" for all other fields when a feature is not found in B on the same chromosome as the feature in A. E.g. none -1 -1 ...
written 8 days ago by microfuge610
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Answer: C: bioinformatics protein PDB ID
... Uniprot provides the id conversion tools from uniprot-> pdb or other structure databases. http://www.uniprot.org/uploadlists/ ...
written 9 days ago by microfuge610
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Comment: C: retrieve Sequence by Gene name?
... Uniprot maintains a list of synonyms for gene names. Gene names can be converted to uniprot ids and then these ids could be used to get other related ids using ID mapping tool http://www.uniprot.org/uploadlists/ . Alternatively ensemble biomart could be used. ...
written 10 days ago by microfuge610
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Comment: C: Homologs between tomato and Arabidopsis
... Ensemble plants biomart is also a good source of orthologs. Also gives dn/ds. ...
written 10 days ago by microfuge610

Latest awards to microfuge

Scholar 11 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
Teacher 11 days ago, created an answer with at least 3 up-votes. For A: chain file for maize
Commentator 9 months ago, created a comment with at least 3 up-votes. For C: Fasta alignment to Tajima's D and population statistics
Supporter 9 months ago, voted at least 25 times.
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: chain file for maize
Centurion 9 months ago, created 100 posts.
Commentator 10 months ago, created a comment with at least 3 up-votes. For C: Fasta alignment to Tajima's D and population statistics
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

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