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Popular Question to
benformatics
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Dan
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Nai
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Arindam Ghosh
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Recent Replies
Comment: How do I explain the difference between edgeR, LIMMA, DESeq etc. to experimental
by
Kevin Blighe
85k
Hello friend. Life moves on...
Comment: How to make the profile line of `deepTools::plotHeatmap` more smooth?
by
Dan
▴
120
Do you mean I should check the intersections between the peaks in the `bed` file using `bedtools intersect` (https://bedtools.readthedocs.i…
Answer: How to make the profile line of `deepTools::plotHeatmap` more smooth?
by
Trivas
★
1.2k
Your issue is with your bed file then, not necessarily with deep tools. I'd look into the bedtools suite to see if you can minimize overlap…
Comment: Filtering mitochondrial reads from ATAC-Seq aligned reads- what to do with reads
by
benformatics
3.6k
I think it would be fair (and conservative) to remove read pairs where one maps to the mitochondrial genome. It should be a relatively very…
Answer: Convert Bam file to Fastq
by
Michael
52k
I think your code is incorrect bash syntax. I think you want something like this:
sort bam_headers.txt > bam_haeders-sorted.txt # c…
Comment: Combination of ROC CURVE
by
Maria17
▴
20
For example, if three targets are combined and the mean value is plotted, the different combinations give different numbers, but there are …
Comment: How do I explain the difference between edgeR, LIMMA, DESeq etc. to experimental
by
Kermit
▴
80
neither simple nor helpful, but perhaps the OP changed his question away from "why might diff models produce diff results" to the current "…
Comment: Convert Bam file to Fastq
by
Michael
52k
At first, I would trust samtools to do the right thing but of course it doesn't hurt to double check. But I think the crux is what is in fa…
Comment: Convert Bam file to Fastq
by
Pierre Lindenbaum
154k
paste fastq1_read_ids.txt fastq2_read_ids.txt is a tabular file with two column. Is it the same for bam_read_names.txt ?
Answer: WGCNA Trait File Issues
by
Jennifer M
•
0
![enter image description here][1]
[1]: /media/images/0cf4eaa7-9550-4bbb-b43e-208dc787
Comment: Pairwise Alignment
by
WouterDeCoster
47k
> for whole genome analysis
What do you mean with that? You provide too little information for us to answer your question.
Comment: Getting species names and taxa id from assembly accession number
by
GenoMax
129k
There must be some temporary glitch.
Following command works (via EntrezDirect):
$ esearch -db assembly -query GCA_000001405.29 | esu…
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