User: Adrian Pelin

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Adrian Pelin2.1k
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4 years, 8 months ago
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Comparative and Population Genomics of Microsporidia. Comparative and Functional Genomics of Cryptomycotans.

Posts by Adrian Pelin

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Comment: C: Anybody Managed To Make Inparanoid Work?
... I find orthoMCL to do the job better, that's why I gave up on inparanoid. ...
written 8 months ago by Adrian Pelin2.1k
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Comment: C: Detecting junctions from reads spanning large indels
... oh I see. Both still do the same thing though, correct? ...
written 8 months ago by Adrian Pelin2.1k
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Comment: C: Detecting junctions from reads spanning large indels
... sweet, goes directly to coordinates. Is there any way to get an intermediary sam file to see which reads were counted for generating coordinates? ...
written 8 months ago by Adrian Pelin2.1k
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Detecting junctions from reads spanning large indels
... Hello, I am mapping my reads with an aligner that allows for large indels (bbmap, other suggestions welcome). I am than using SamJs to get reads that have large indels >1kb java -jar ${HOME}/programs/jvarkit/dist/samjs.jar --file get_indel_sam_filter.javascript --samoutputformat SAM -o Fas ...
dna-seq sam written 8 months ago by Adrian Pelin2.1k • updated 8 months ago by Pierre Lindenbaum110k
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Comment: C: Filter sam file to remove reads with large deletions
... Neat tool Pierre, I want to do the opposite, I want to find reads in sam file that span large deletions (>1kb), so I thought I would use your -X option, to save discarded. Running into a few issues, samoutputformat is not considered valid and -X doesn't get recognized? https://pastebin.com/k2dVRx ...
written 8 months ago by Adrian Pelin2.1k
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Comment: C: bedtools merge - removing features completly overlapped by other features
... Eureka! Works amazing. Indeed very important to not forget sort-bed! ...
written 10 months ago by Adrian Pelin2.1k
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Comment: C: bedtools merge - removing features completly overlapped by other features
... Thanks, getting closer. Your example seems to be working flawlessly (I have recreated A.bed and tried the command), but when I try it on my annotation, I lose any features that overlap with each other. Consider your example, if we were to add "chr1 80-101 id-0", we would lose all entries but the las ...
written 10 months ago by Adrian Pelin2.1k
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Comment: C: bedtools merge - removing features completly overlapped by other features
... There is only one file to begin with. I tried specifying the file twice for A and B and ended up getting every entry as a duplicate from the original file. ...
written 10 months ago by Adrian Pelin2.1k
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bedtools merge - removing features completly overlapped by other features
... Hello, Assuming we start with only one bed file, example: F1 ------------------------- F2 ---- F3 ---- F4 -------------- Default bedtools merge behaviour will output one sole feature spanning from F1 start to F4 end, since F1 and F4 o ...
bedtools written 10 months ago by Adrian Pelin2.1k
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Comment: C: Phylogeny: tree branch length on a log scale
... Great idea! It took a little playing around with. Turns out, most branch distances are below 1 in numerical values... who would have thought? so naturally the first tree looked really funny with branches extending to the left as a result of taking the log of sub 1 values. To get around this I esse ...
written 11 months ago by Adrian Pelin2.1k

Latest awards to Adrian Pelin

Popular Question 7 months ago, created a question with more than 1,000 views. For MLE Approach: Calculate LD (r^2) from unphased data
Popular Question 7 months ago, created a question with more than 1,000 views. For MLE Approach: Calculate LD (r^2) from unphased data
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