User: abascalfederico

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Posts by abascalfederico

<prev • 149 results • page 1 of 15 • next >
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Comment: C: Help with CD-hit commands for DNA sequences
... Mine is version 4.5.4, but I've checked more recent versions still use -c ...
written 11 days ago by abascalfederico850
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Answer: C: Help with CD-hit commands for DNA sequences
... Hi, In the version I have the maximum % identity is controlled through "-c" -c sequence identity threshold, default 0.9 this is the default cd-hit's "global sequence identity" calculated as: number of identical amino acids in alignment divided by the full length of the shorter sequenc ...
written 12 days ago by abascalfederico850
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Comment: C: Question about MD tag in BAM file
... Thanks Devon, It's strange... Looking at the cigar string in the CIGAR column and the MD tag, I have realised that all those cases unexpected to me are related to insertions in the read. For instance, the MD=74 posted before is associated to 50M1I24M. In contrast, deletions are well described in the ...
written 13 days ago by abascalfederico850
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Question about MD tag in BAM file
... Hi, There are some MD tags I do not understand. I find no problems understanding most of them, but in some cases the NM (number of mismatches) says there is 1 mismatch and the MD tag is simply "74" (instead of, for example, something like 56A17, 3T71, etc). How is it possible that there is a misma ...
bam md written 13 days ago by abascalfederico850
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Comment: C: ClustalW modifies the input sequence
... It does not seem very reasonable to not let gaps in your first sequence, does not make sense from a biological/evolutionary perspective. I would let clustalw (or Mafft, Muscle... and other better aligners) to insert the gaps they consider appropriate and then remove all the columns that have a gap i ...
written 13 days ago by abascalfederico850
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Comment: C: Definition of PCR duplicates based on alignment coordinates
... What I've found out so far... I do not have an exact answer but it seems available software mark duplicates by comparing only 5' coordinates (including clipping if present). If paired reads are at hand, the 5' coordinates of the first and second mates have to be identical (with respect to another pa ...
written 17 days ago by abascalfederico850
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Definition of PCR duplicates based on alignment coordinates
... Dear all, I have to identify PCR duplicates by myself and would like to understand how tools like Picard's MarkDuplicates and Samtools' rmdup define them. Do they require that the beginning and end alignment coordinates are the same? I was thinking that since the quality of reads usually degrades ...
pcr duplicates written 19 days ago by abascalfederico850
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Comment: C: Subdivide phylogenetic trees
... You could use what jrj.healey suggested. If you compute RF distances for all tree pairs, you would be able to make groups of trees that have RF=0 (same topology) ...
written 26 days ago by abascalfederico850
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Comment: C: Phylogenetic Tree to compare my sequences to a database
... Although I haven't gone through the paper my guess is that it depends. In my experience cleaning alignments has solved problems in phylogenetic reconstruction, and this makes perfect sense from a theoretical perspective: any extraneous sequence or badly align region can confound phylogenetic reconst ...
written 27 days ago by abascalfederico850
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Comment: C: what is pairwise dN/dS used for?
... Nope. You have the same problem between chimp and mouse than between human and chimp, you cannot be sure which one accumulated substitutions, you can imagine complex scenarios (e.g. positive selection in chimp and mouse). That's the problem with pairwise comparisons. ...
written 27 days ago by abascalfederico850

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Popular Question 5 days ago, created a question with more than 1,000 views. For F3 test for admixture
Commentator 4 weeks ago, created a comment with at least 3 up-votes. For C: Is it good practice to convert lowewst quality genotyes to missing?
Scholar 8 weeks ago, created an answer that has been accepted. For A: How to properly merge multiple runs into one bam file ?
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: distance between two genes
Scholar 5 months ago, created an answer that has been accepted. For A: How to properly merge multiple runs into one bam file ?
Student 5 months ago, asked a question with at least 3 up-votes. For Samtools' mpileup with pysam: enabling and disabling BAQ probabilistic realignment
Scholar 5 months ago, created an answer that has been accepted. For A: How to properly merge multiple runs into one bam file ?
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Commentator 12 months ago, created a comment with at least 3 up-votes. For C: Is it good practice to convert lowewst quality genotyes to missing?
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Scholar 12 months ago, created an answer that has been accepted. For A: How to properly merge multiple runs into one bam file ?
Scholar 12 months ago, created an answer that has been accepted. For A: How to properly merge multiple runs into one bam file ?
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: distance between two genes
Scholar 13 months ago, created an answer that has been accepted. For A: How to properly merge multiple runs into one bam file ?
Scholar 13 months ago, created an answer that has been accepted. For A: How to properly merge multiple runs into one bam file ?
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