Questions tagged [merge]
As a command 'merge' relates to merging two dataframes in either R or Python's pandas
16
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Merging regions according to their identifier
I have a huge file (20 GB) which has a range of genomic locations, and for each location there is an identifier(4th column), ...
- 171
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3
answers
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Is it possible to merge scRNAseq data from experiments with different design?
I have 4 different single-cell RNAseq experiments, each one representing a different sample of cell type population. I'd like to merge them to a single dataset. However, different cell types are ...
- 1,813
4
votes
1
answer
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Merge the dataframes with python iterator
I have 3 experiment files (File1.tsv, File2.tsv, File3.tsv) from three experiments and 1 library file (library_file.tsv). I want ...
- 317
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votes
3
answers
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Strategy for merging many VCFs
Can anyone suggest a strategy for speeding up VCF merging?
I have ~44,000 single-sample VCFs that I am trying to merge into a multi-sample VCF with bcftools merge, ...
- 713
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How to remove redundancy from a gtf file?
I have an annotation file. I would like to remove redundancy, as shown in the example (in the real file, I have a lot of these redundant cases).
I would like to consider only one of the following ...
- 161
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3
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Merging multiple seurat datalist together
I have a R script that subsets out the tumor cells from 6 different individual seurat objects.
It gets a list of file paths for all RDS files containing the expression data for multiple datasets in a ...
- 391
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votes
3
answers
170
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How to merge multiple list into a single dataframe replacing common values with 1 -python
I have multiple lists on python:
...
- 161
2
votes
1
answer
5k
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How to resolve Error in fix.by(by.x, x) : 'by' must specify a uniquely valid column while using merge function in R
I have two csv formatted data frames that I want to merge. First data frame contains 9 columns and the second contains three columns. Based on column names: start, end, function I am trying to merge ...
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0
answers
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bcftool merge of 5K samples makes ID a large string
I am using bcftools to merge 5000+ vcf files using this command
bcftools merge -l list_of_vcfs.txt
I am getting the following error
...
- 21
2
votes
0
answers
267
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Subsetting out prefix from genes and merging
I'm working with PTX samples (human and mouse), they're aligned to both transcriptomes and so gene names contain hg38- and mm10- at the beginning of each gene. I have eliminated teh prefixes because I ...
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1
vote
2
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568
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Large amount of REF prefix differences after lifting
I lifted some unmerged trio files from hg19 to hg38 using liftOverPlink. It looks like that several houndred allels on each chromosome of one file shifted/switched to non-standard alleles. I recorded ...
- 145
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Title: Error merging VCF files: "The REF prefixes differ: G vs A"
I'm trying to merge two VCF files, but I'm running into an error message that says ...
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votes
2
answers
227
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merge rows (to columns) in R dataframe based on IDs
I have a dataframe with two columns: $1 = transcript ID, $2 = expression counts (tpm). This comes from a merging of several ...
- 2,706
0
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1
answer
138
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Impact of merging ChIP-seq runs of the same sample on PCR duplicates identification?
I'd like to a follow up question to this question related to merging fastq files for ChIP-seq.
Let's assume we have one sample library that is re-sequenced two or three times in order to achieve a ...
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-1
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2
answers
522
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Merge data frame on either of the 2 columns in R or python
I have two data frames. One data frame with one column and second data frame with two columns. I need to merge first data frame with either column of the second data frame and returns the values. ...
user14023
-2
votes
1
answer
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Making a union data from different list of genes
I have two groups of patients
I have a list of driver genes
Clearly each group have mutation in a subset of these gene some of which are common between two groups and some of which are unique to one ...
- 2,232