User: Mensur Dlakic

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Mensur Dlakic5.3k
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http://www.montana.edu...
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Posts by Mensur Dlakic

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Comment: C: sequencing depth vs quality assembly
... That is correct. Everything is explained in the protocol. ...
written 1 day ago by Mensur Dlakic5.3k
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Answer: A: sequencing depth vs quality assembly
... [**khmer**][1] can do [**digital normalization**][2] to 50x, though 100x is not too crazy in terms of sequencing depth. [1]: https://khmer.readthedocs.io/en/latest/ [2]: https://khmer-protocols.readthedocs.io/en/v0.8.2/mrnaseq/2-diginorm.html ...
written 2 days ago by Mensur Dlakic5.3k
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Comment: C: Versioning of Blast DB and Reproducible Research
... > If you clearly mention what, how and when you used data or tools, you at least provide the possibility to reproduce it (in contrast to for instance simply mention "we used nr" ) Some authors preserve the exact database they used to create manuscript results, and make it available for download. ...
written 2 days ago by Mensur Dlakic5.3k
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Answer: A: Versioning of Blast DB and Reproducible Research
... It depends on whether you want reproducibility for the sake of principle, or if you have a particular goal in mind. Sequence names and IDs don't change, so that part is reproducible. BLAST scoring shouldn't change much either, and that could be an issue when changing program versions rather than upd ...
written 2 days ago by Mensur Dlakic5.3k
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Answer: A: Error when trying to unzip fastqc file that i got using wget
... Either the file was download incorrectly, or you don't have a current enough version of `unzip`. Here is the MD5 checksum of that same file when I download it: md5sum fastqc_v0.11.9.zip output: ee7901b681bb2762d75d5a56c7ec6958 fastqc_v0.11.9.zip Next, try file type: file fastqc_v0.11 ...
written 3 days ago by Mensur Dlakic5.3k
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Comment: C: Running Blastall Before MCL for Paralog Clustering
... From what I understand, your goal is to cluster paralogs from 13 different genomes. That means concatenating all genomes together, doing all-vs-all blast search, and finally MCL clustering. Concatenation (typing only 3 genome names): cat genome_01.fas genome_02.fas genome_03.fas > all_genom ...
written 4 days ago by Mensur Dlakic5.3k
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Answer: A: Clarification for using PSI-BLAST to generate a PSSM (am I doing it right?)
... From what I can tell, there are at least two things that you are doing wrong. First, it seems that your query file has multiple sequences. If that's indeed the case, `psiblast` will search with each sequence individually (and sequentially), and each search will overwrite the results of previous. Th ...
written 4 days ago by Mensur Dlakic5.3k
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Answer: A: Running Blastall Before MCL for Paralog Clustering
... > I am confused on how to do this step as it is has not worked for me so far. What exactly did you try? Has it not worked because of incorrect blast installation, or you don't know how to formulate the command? If the latter, try this: blastall -p blastp -i seq.fas -d seq.fas -m8 -o seq.cbl ...
written 5 days ago by Mensur Dlakic5.3k
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Answer: A: How to interpret alignment scores ?
... Generally speaking, that is a good score. However, alignment scores are length-dependent, so for a really long alignment - say 10 thousand nucleotides - this would not be a good score. You can in fact see what scores these two sequences would get when aligned against the same sequence by putting the ...
written 6 days ago by Mensur Dlakic5.3k
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Answer: A: How to extract the longest protein per gene from a multifast file.
... [**CD-HIT**][1] will do this automatically as part of its redundancy removal procedure. It clusters the sequences according to a given identity cutoff (90% is default), and for each cluster will retain only the longest sequence. Super fast, easy to install and run. [1]: http://weizhongli-lab.org ...
written 6 days ago by Mensur Dlakic5.3k

Latest awards to Mensur Dlakic

Teacher 5 days ago, created an answer with at least 3 up-votes. For C: Read length for metagenomics analysis
Scholar 5 days ago, created an answer that has been accepted. For A: Prottest output to Raxml input
Scholar 5 days ago, created an answer that has been accepted. For A: Prottest output to Raxml input
Commentator 13 days ago, created a comment with at least 3 up-votes. For C: PCA cannot separate different breeds
Teacher 13 days ago, created an answer with at least 3 up-votes. For C: Read length for metagenomics analysis
Scholar 13 days ago, created an answer that has been accepted. For A: Prottest output to Raxml input
Scholar 22 days ago, created an answer that has been accepted. For A: Prottest output to Raxml input
Teacher 22 days ago, created an answer with at least 3 up-votes. For C: Read length for metagenomics analysis
Commentator 25 days ago, created a comment with at least 3 up-votes. For C: PCA cannot separate different breeds
Teacher 27 days ago, created an answer with at least 3 up-votes. For C: Read length for metagenomics analysis
Teacher 27 days ago, created an answer with at least 3 up-votes. For A: Performing Hmmer search against pfam versus UniRef100
Commentator 27 days ago, created a comment with at least 3 up-votes. For C: PCA cannot separate different breeds
Scholar 28 days ago, created an answer that has been accepted. For A: Prottest output to Raxml input
Scholar 4 weeks ago, created an answer that has been accepted. For A: Prottest output to Raxml input
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For C: Read length for metagenomics analysis
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For C: Read length for metagenomics analysis
Scholar 5 weeks ago, created an answer that has been accepted. For A: Prottest output to Raxml input
Scholar 5 weeks ago, created an answer that has been accepted. For A: Prottest output to Raxml input
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For C: Read length for metagenomics analysis
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For C: Read length for metagenomics analysis
Scholar 6 weeks ago, created an answer that has been accepted. For A: Prottest output to Raxml input
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Performing Hmmer search against pfam versus UniRef100
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For C: Read length for metagenomics analysis
Scholar 6 weeks ago, created an answer that has been accepted. For A: Family ID/Name in PANTHER
Scholar 6 weeks ago, created an answer that has been accepted. For A: Prottest output to Raxml input

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