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edus_bioinfo
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barslmn
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tarek.mohamed
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Recent Replies
Answer: What type of normalization did they use in this article?
by
Matthias Zepper
3.7k
> Transcriptomic analysis
>
> [...] We subsequently filtered genes that
> were not expressed in any of the samples (in each cohort
> indep…
Comment: How to get a comperative result of 2 bed files?
by
Pierre Lindenbaum
154k
what kind of measurement do you need ? I see one bed file in your description , what are the TWO bed file ?
Answer: MACS2 peak calling
by
Maurice
•
0
Thank you!
And for what regards peaks annotation, how can the tool I'm going to use assign peaks to the correct location without knowing t…
Comment: sorting BAM file
by
ATpoint
72k
You can simply use `samtools sort` to get rid of this read group nonsense these Broad institute tools always complain about.
Answer: Which type of variant caller should I use in a WES normal cell line sample?
by
ATpoint
72k
Any variant caller will do. Somatic calling is usually an additional mode while calling without matched normal is typically always possible.
Comment: Create customized gene annotation file
by
ATpoint
72k
Plese confirm whether you read and tried the manual: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/…
Answer: MACS2 peak calling
by
ATpoint
72k
Yes, that is correct. Peaks from experiments such as ChIP-seq or ATAC-seq are based on DNA, which is double-stranded and unlike RNA (where …
Answer: Alignment of case vs. control from different origin
by
i.sudbery
17k
I hate to be the one to tell you this, but the reason you have been unable to find an answer isnthat what you are trying to do is not gener…
Answer: Peaks annotation on bacterial genome
by
Maurice
•
0
Thank you for your kind reply!
I have just a further question. Which is the difference between using annoPeaks and annotatePeaksinbatch wi…
Comment: Dada2 in Qiime2: losing reads during merging
by
kamanovae
▴
80
Thanks for the answer!
I requested information from the lab. Indeed, a region was sequenced that does not overlap with such short reads o…
Answer: CluserProfiler message "No gene can be mapped"
by
13554221497
•
0
use_internal_data=TRUE
the kegg analysis need read KEGG annotation online, so if your network is bad, the analysis maybe failed;
…
Comment: CluserProfiler message "No gene can be mapped"
by
13554221497
•
0
use_internal_data=TRUE, add the params maybe can solve the problem.
KEGG analysis need reading KEGG annotation online, so if your netw…
Comment: Concatenating text files based on common indices
by
Mensur Dlakic
★
23k
> 'str' object has no attribute 'merge'
It appears you are trying to merge file names rather than dataframes. You have to read in those f…
Answer: Selecting Random Pairs From Fastq?
by
sebastian.gregoricchio
▴
30
I believe that the easiest option for paired-end data is to use `fastq-sample` from fastq-tools:
```
fastq-sample -n 5000000 pair_R1.fa…
Comment: minimap's SAM file MAPQ value for the unique alignments
by
WouterDeCoster
47k
It always depends on what you want to do with the data.
> to the reference database
That is not too specific, do you mean genome, transcr…
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