6
votes
Merging regions according to their identifier
If I understand correctly, you could create dummy chromosomes made by merging chromosome and identifier, merge with bedtools, split back chromosomes and identifiers. E.g.
...
- 689
4
votes
Strategy for merging many VCFs
We created this over the pandemic when we needed to merge loads of VCFs which all have the same header and first few columns (ie same variants)
https://github.com/iqbal-lab-org/ivcfmerge
That page ...
- 41
3
votes
Merging regions according to their identifier
Here is a fairly simple (and hopefully readable) native Python solution. It assumes that the bed file is sorted prior to parsing:
...
- 3,928
3
votes
Strategy for merging many VCFs
I ended up using an iterative approach (inspired by this post), which took 1.5 hours - so a massive speed up (and that was just the sequential version).
Note: fd is ...
- 663
3
votes
Accepted
Merging regions according to their identifier
The following python script will do what you want and should be relatively memory efficient. It processes a single chromosome at a time, so either sort the input or ensure that at least entries in a ...
- 19.5k
3
votes
Accepted
Merging multiple seurat datalist together
The first parameter of merge should be a Seurat object, the second (y) can be one Seurat object or a list of several. Try:
...
- 252
2
votes
Merging multiple seurat datalist together
You should be able to use something like this:
Reduce(
f = function(x, y) {merge(x, y, merge.data = FALSE)},
x = datasets # list of Seurat objects
)
This ...
- 3,892
2
votes
Accepted
2
votes
Is it possible to merge scRNAseq data from experiments with different design?
See this paper from the Marioni group, where they propose a method for correcting batch effects between single cell sequencing experiments when each experiment contains different sub-populations:
...
- 3,271
2
votes
Accepted
Is it possible to merge scRNAseq data from experiments with different design?
It’s right there on the cellranger manual:
#aggregate results of counts for separate samples
cellranger aggr
#analyse the combined results
cellranger reanalyze
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- 873
1
vote
Strategy for merging many VCFs
Perform a tree based merge of the files.
Sort the files into groups that can easily be merged in a measurable amount of time.
Merge each group into a separate Variant Call Format (VCF) file
Has the ...
- 111
1
vote
Is it possible to merge scRNAseq data from experiments with different design?
Have you tried seurat3? Here is the reference:
https://satijalab.org/seurat/v3.0/pancreas_integration_label_transfer.html
1
vote
Merge data frame on either of the 2 columns in R or python
I think this question is more about subsetting than merging. You can try this solution in R:
...
- 313
1
vote
Accepted
Large amount of REF prefix differences after lifting
It is important that after lifting over a VCF/BCF file from one coordinate system to another, the header of the resulting file contains the chromosome/contig names as present in the coordinate system ...
- 750
1
vote
Impact of merging ChIP-seq runs of the same sample on PCR duplicates identification?
If you are sequencing same library multiple times (as you state in the question), any read that appears in multiple sequencing runs is likely to have been generated via PCR duplication from the same ...
- 3,271
1
vote
Accepted
Making a union data from different list of genes
Maybe something like this:
df = merge(
data.frame(gene=rownames(d1),d1),
data.frame(gene=rownames(d2),d2),all=TRUE)
If you want to replace NA with 0:
...
- 1,678
1
vote
merge rows (to columns) in R dataframe based on IDs
For that purpose, you may also use the reshape2 R package which allows you to switch wide to long format for data.frames. However, for that, you need an additional column with sample identifiers, e.g.:...
1
vote
Accepted
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