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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. ...
dariober's user avatar
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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 ...
Zamin Iqbal's user avatar
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: ...
Chris_Rands's user avatar
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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: ...
Cloudberry's user avatar
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 ...
Devon Ryan's user avatar
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2 votes
Accepted

Merge the dataframes with python iterator

Its a simple join operation. ...
M__'s user avatar
  • 10.3k
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: ...
Ian Sudbery's user avatar
  • 3,271
2 votes
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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 ...
Tom Kelly's user avatar
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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 ...
haci's user avatar
  • 3,692
2 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 ...
Michael Hall's user avatar
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 ...
G. Putnam's user avatar
  • 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
Zhi-Ping Feng's user avatar
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: ...
Nitesh Shriwash's user avatar
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 ...
JRodrigoF's user avatar
  • 705
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 ...
Ian Sudbery's user avatar
  • 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: ...
StupidWolf's user avatar
  • 1,668
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.:...
thomas duge de bernonville's user avatar
1 vote
Accepted

merge rows (to columns) in R dataframe based on IDs

For a data.frame named foo: ...
Devon Ryan's user avatar
  • 19.5k

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