User: jomo018

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jomo018300
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Posts by jomo018

<prev • 51 results • page 1 of 6 • next >
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Answer: A: Building bioinformatics tools in Ubuntu 17.10
... It is just a new warning in compiler GCC 6. Intended for programmers, probably those writing in both C++ and Python, where command indentation has different meaning. I would guess program behaviour (or misbehaviour...) would be exactly same as before. ...
written 21 days ago by jomo018300
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Comment: C: Why does read quality drop after adapter trimming with cutadapt?
... The lower bound of the box plot (lower whisker) is not the minimal observable value. The exact definition varies. It may represent the tenth percentile for example. If the raw plot of adapter contamination shows high values (say above 50%), the processed box plot may possibly be showing the raw outl ...
written 4 weeks ago by jomo018300
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Answer: A: A doubt about the clinical information of hepatocellular carcinoma in TCGA
... 1. Browse to: [https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search][1] 2. Enter *Search* terms: **vascular tumor cell** 3. Browser will suggest: *"vascular tumor cell invasion type"*, select it and click *Search*. 4. Under *Search Results* click on *"vascular tumor cell inva ...
written 6 weeks ago by jomo018300
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Comment: C: Windows/Linux computer partitioning for RNAseq
... Actually windows 10 directy supports ubunto bash shell. It works good. ...
written 7 weeks ago by jomo018300
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Answer: C: Why names() returns empty?
... Make sure **datExpr** is a data frame rather than matrix which will respond with NULL. E.g. check: `names(data.frame(datExpr))` ...
written 7 weeks ago by jomo018300
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Comment: C: bedtools fisher interpretation of "in -a" "not in -b"
... The genome file is just a list of CHR sizes. Here is the section containing CHR1 through CHR3 which is relevant for the examples above: chr1 248956422 chr10 133797422 chr11 135086622 chr11_KI270721v1_random 100316 chr12 133275309 chr13 114364328 chr14 107043718 chr14 ...
written 9 weeks ago by jomo018300
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Comment: C: bedtools fisher interpretation of "in -a" "not in -b"
... Just to clarify, `bedtools intersect` does report correctly only overlapping peaks and ignores non-overlapping peaks like the ones above. ...
written 9 weeks ago by jomo018300
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Comment: C: bedtools fisher interpretation of "in -a" "not in -b"
... Genome is hg38. Here is an example of non-overlappers: From File a: chr1 28641883 28645188 1_MACS_peak_686_lociStitched 521 . chr1 28881968 28903124 6_MACS_peak_699_lociStitched 66 . **chr1 30718699 30738774 6_MACS_peak_715_lociStitched 621** . chr1 30759728 30784018 8_MACS_pea ...
written 9 weeks ago by jomo018300
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Comment: C: bedtools fisher interpretation of "in -a" "not in -b"
... Thank you Kevin. The files are all sorted as required. I have posted the command so you can see I am just using default values. The problem is that any constraints on -f, -r, -s and -S will further ***reduce*** overlaps and ***increase*** non-overlapping peaks. But I already have 150 non-overlappin ...
written 9 weeks ago by jomo018300
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bedtools fisher interpretation of "in -a" "not in -b"
... I am using **bedtools fisher** as follows: > bedtools fisher -a $fA -b $fB -g $fG > $fOut Where fA consists of wide peaks and fB narrower peaks. The results are: Number of query intervals: 741 Number of db intervals: 18079 Number of overlaps: 1481 Number of possible inte ...
bedtools intersection fisher written 9 weeks ago by jomo018300

Latest awards to jomo018

Scholar 4 weeks ago, created an answer that has been accepted. For A: Illumina paired-end reads R1 and R2 mixed together?
Scholar 7 weeks ago, created an answer that has been accepted. For A: Illumina paired-end reads R1 and R2 mixed together?
Scholar 9 weeks ago, created an answer that has been accepted. For A: Illumina paired-end reads R1 and R2 mixed together?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Illumina paired-end reads R1 and R2 mixed together?
Commentator 9 months ago, created a comment with at least 3 up-votes. For C: Why not merging?
Scholar 13 months ago, created an answer that has been accepted. For A: Illumina paired-end reads R1 and R2 mixed together?
Teacher 13 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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