User: jomo018

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jomo018180
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Posts by jomo018

<prev • 32 results • page 1 of 4 • next >
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Comment: C: Problem with methylKit and Bismark
... Suggest you show the script lines preceding and including methRead. Please Format the lines with the proper icon. ...
written 10 days ago by jomo018180
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Comment: C: vcf2bed giving empty bed file as output
... Wild guess: wrong path to input file. What's your exact command line? ...
written 11 days ago by jomo018180
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Answer: A: Please clarify me about countOverlaps()?
... Actually, these sentences refer specifically to the following **two** commands: hits <- countOverlaps(h1b, txdb) ol <- countOverlaps(txdb, h1b[hits==1]) The first command counts overlaps with txdb elements (e.g. genes) per each read in h1b. In the second command, only h1b items cha ...
written 12 days ago by jomo018180
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Answer: A: How to remove the empty line in using python
... The lines you read include the end-of-line (eol) from the input file. The print command adds its own end-of-line. So you end up with two eol hence one blank line. You can fix this using strip() on the line you read. For example line.strip() will discard eol from line. ...
written 12 days ago by jomo018180
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Answer: A: problem in fastq-dump of SRA file
... Include the path of fastq.sra. For example: fastq-dump ./fastq.sra --split-3 -I ...
written 20 days ago by jomo018180
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Answer: A: Problem with methylKit and Bismark
... Two step solution: Use coverage2cytosine to convert .cov file to an intermediate file. Then a one-liner awk command or some other script to convert the intermediate file to a methRead input file. The reason for this two-step process is that .cov lacks strand information. cov file format: ...
written 7 weeks ago by jomo018180
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Comment: C: Converting TCGA Bam files to fastq: Picard does not work!
... In BWA site I see this Q/A: > **With BWA-MEM/BWA-SW, my tools are complaining about multiple primary alignments. Is it a bug?** > It is not. Multi-part alignments are possible in the presence of > structural variations, gene fusion or reference misassembly. However, > representing m ...
written 5 months ago by jomo018180
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Comment: C: Converting TCGA Bam files to fastq: Picard does not work!
... Do you know which aligner created the BAM? I have found BAM to FASTQ conversion almost impossible in some cases of BAMs originating from RNA-SEQ. I believe its related to conflicting interpretations of mates and pairs. ...
written 5 months ago by jomo018180
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Comment: C: Why not merging?
... Well, the consensus here seems to be that pre-merging is good. So I'll just add my two-cents as to the claim that pre-merging may **inherently** lose information, irrespective of aligners and mergers. A merger employs **two** pieces of information which are available to it: two sequenced reads. When ...
written 6 months ago by jomo018180
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Answer: A: Why not merging?
... By pre-merging, you may actually be losing information. For example, if the pairs do not agree on a specific base, the merged fragment would most likely report the base of higher quality and possibly report it along with the lower quality. That lower quality might still be high though. When feeding ...
written 6 months ago by jomo018180

Latest awards to jomo018

Teacher 12 days ago, created an answer with at least 3 up-votes. For A: Illumina paired-end reads R1 and R2 mixed together?
Commentator 6 months ago, created a comment with at least 3 up-votes. For C: Why not merging?
Scholar 9 months ago, created an answer that has been accepted. For A: Illumina paired-end reads R1 and R2 mixed together?
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Illumina paired-end reads R1 and R2 mixed together?

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