Questions tagged [merge]

As a command 'merge' relates to merging two dataframes in either R or Python's pandas

Filter by
Sorted by
Tagged with
2 votes
0 answers
31 views

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 ...
bioinfo_comp's user avatar
2 votes
3 answers
1k views

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 ...
mmpp's user avatar
  • 371
3 votes
3 answers
2k views

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, ...
Michael Hall's user avatar
1 vote
0 answers
118 views

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 ...
El K's user avatar
  • 11
3 votes
1 answer
128 views

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 ...
Riya's user avatar
  • 307
-2 votes
2 answers
265 views

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. ...
Nithya Chandramohan's user avatar
2 votes
1 answer
2k views

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 ...
kumuda's user avatar
  • 23
1 vote
2 answers
370 views

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 ...
mugdi's user avatar
  • 145
2 votes
3 answers
103 views

How to merge multiple list into a single dataframe replacing common values with 1 -python

I have multiple lists on python: ...
Marco's user avatar
  • 161
3 votes
0 answers
224 views

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 ...
Marco's user avatar
  • 161
2 votes
0 answers
212 views

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 ...
mmpp's user avatar
  • 371
0 votes
1 answer
105 views

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 ...
Ni-Ar's user avatar
  • 1
-2 votes
1 answer
62 views

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 ...
Angel's user avatar
  • 1,981
0 votes
2 answers
207 views

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 ...
aechchiki's user avatar
  • 2,676
6 votes
4 answers
735 views

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), ...
bapors's user avatar
  • 171
5 votes
3 answers
4k views

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 ...
gc5's user avatar
  • 1,783