User: abascalfederico

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Posts by abascalfederico

<prev • 154 results • page 1 of 16 • next >
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Comment: C: bedtools intersect bed and vcf, coordinates problem
... Ok, I know what's happening... Those sites are indels and bedtools, smartly (not as me), is taking that into account! Thanks for your help. I run it like this: intersectBed -a file.bed -b file.vcf Version v2.22.0 Contents of "file.bed": 1 100 101 Contents of "file.vcf": ##fileform ...
written 18 days ago by abascalfederico860
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Comment: C: bedtools intersect bed and vcf, coordinates problem
... Thanks WouterDeCoster. However, that doesn't answer my question. According to what is explained in that post I should get only one intersection between my 0-based bed and my 1-based vcf. ...
written 18 days ago by abascalfederico860
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bedtools intersect bed and vcf, coordinates problem
... I've found something unexpected, may be I just didn't understand how coordinates work. I am intersecting a bed file with coordinates: 1 100 101 Against a vcf file, which has two sites in it: 1 100 etc etc 1 101 etc etc The bed coordinates define a sin ...
bedtools bed vcf written 18 days ago by abascalfederico860
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Comment: C: Questions about LB field in SAM specification for PCR duplicate removal
... Library is the DNA library, the preparation of DNA, where PCR duplicates arise. It doesn't matter if you run it on different lanes, you should treat all the reads from a library together when marking read duplicates. ...
written 20 days ago by abascalfederico860
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Comment: C: Questions about LB field in SAM specification for PCR duplicate removal
... I have faced a similar problem in the past. From what I know MarkDuplicates looks for duplicates within reads that belong to the same read group (RG), possibly checking the library part of the RG. All the data from the same library should have the same library in the RG. However, when you analyse yo ...
written 20 days ago by abascalfederico860
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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 5 weeks ago by abascalfederico860
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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 5 weeks ago by abascalfederico860
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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 6 weeks ago by abascalfederico860
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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 6 weeks ago by abascalfederico860
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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 6 weeks ago by abascalfederico860

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Popular Question 4 weeks ago, created a question with more than 1,000 views. For F3 test for admixture
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Scholar 3 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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Scholar 6 months ago, created an answer that has been accepted. For A: How to properly merge multiple runs into one bam file ?
Student 6 months ago, asked a question with at least 3 up-votes. For Samtools' mpileup with pysam: enabling and disabling BAQ probabilistic realignment
Scholar 6 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 13 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 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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Scholar 14 months ago, created an answer that has been accepted. For A: How to properly merge multiple runs into one bam file ?
Scholar 14 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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