User: jomo018

gravatar for jomo018
jomo018330
Reputation:
330
Status:
Trusted
Location:
Last seen:
2 days, 8 hours ago
Joined:
2 years, 5 months ago
Email:
j******@gmail.com

Posts by jomo018

<prev • 53 results • page 1 of 6 • next >
2
votes
1
answer
123
views
1
answer
Information required for Human lncRNA array V6.0, 4 X 180 K, Agilent, ID: 74348
... I am looking for detailed information (probe ID, probe coordinates, ID mapping data) for: > Human lncRNA array V6.0 (4×180 K, Agilent, ID: 74348) Quoted in an online paper. Any ideas on how to gather this information? ...
agilent micro array lncrna written 11 weeks ago by jomo018330 • updated 11 weeks ago by genomax52k
1
vote
1
answer
224
views
1
answers
Answer: A: Pearson correlation between chIP-seq replicates is very poor- am I doing somethi
... Consider the following: 1. Deeptools bamCompare to create a bedgraph file comparing treated sample against input. The tool supports various normalization options. Just beware, when activating ignoreDuplicates, normalization applies to the reads including duplicates. In that case you need to apply p ...
written 12 weeks ago by jomo018330
0
votes
3
answers
314
views
3
answers
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 3 months ago by jomo018330
0
votes
1
answer
275
views
1
answers
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 3 months ago by jomo018330
2
votes
1
answer
312
views
1
answers
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 4 months ago by jomo018330
1
vote
1
answer
275
views
1
answers
Comment: C: Windows/Linux computer partitioning for RNAseq
... Actually windows 10 directy supports ubunto bash shell. It works good. ...
written 4 months ago by jomo018330
2
votes
1
answer
243
views
1
answers
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 4 months ago by jomo018330
0
votes
0
answers
305
views
0
answers
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 5 months ago by jomo018330
0
votes
0
answers
305
views
0
answers
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 5 months ago by jomo018330
0
votes
0
answers
305
views
0
answers
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 5 months ago by jomo018330

Latest awards to jomo018

Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Illumina paired-end reads R1 and R2 mixed together?
Scholar 4 months ago, created an answer that has been accepted. For A: Illumina paired-end reads R1 and R2 mixed together?
Scholar 4 months ago, created an answer that has been accepted. For A: Illumina paired-end reads R1 and R2 mixed together?
Scholar 5 months ago, created an answer that has been accepted. For A: Illumina paired-end reads R1 and R2 mixed together?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Illumina paired-end reads R1 and R2 mixed together?
Commentator 12 months ago, created a comment with at least 3 up-votes. For C: Why not merging?
Scholar 16 months ago, created an answer that has been accepted. For A: Illumina paired-end reads R1 and R2 mixed together?
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Illumina paired-end reads R1 and R2 mixed together?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1879 users visited in the last hour