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Showing top results for tag: Loop • reset
4
votes
6
replies
711
views
Protein loops
protein Loop
11 months ago by Curious ▴ 10
2
votes
2
replies
538
views
move fasta and fastq files with the same name folder
for loop
12 months ago by cabraham03 ▴ 30
2
votes
3
replies
1.1k
views
Removing four columns with the same name and position from 38 data.frames in R
Loop remove R columns data.frame
updated 21 months ago by 12k • written 21 months ago by ▴ 30
4
votes
9
replies
1.7k
views
Aligning fastq files using STAR
RNA loop STAR HG Sequencing
2.2 years ago by kcarey • 0
0
votes
0
replies
417
views
Heteroduplex identification
Heteroduplex loop identification
2.2 years ago by Roy.anupama11 • 0
0
votes
4
replies
1.2k
views
What is the best time saving way to loop over column elements in pandas DF and replace Nan with specific element from each column?
column loop nohup
updated 2.3 years ago by 149k • written 2.3 years ago by • 0
0
votes
1
reply
584
views
Find and replace
sed while loop replace find
updated 2.3 years ago by 12k • written 2.3 years ago by ▴ 50
7
votes
5
replies
1.3k
views
For loop to go over all files in a folder to execute after qc
bash loop script
updated 2.3 years ago by 149k • written 2.3 years ago by ▴ 10
0
votes
2
replies
1.1k
views
Loop for Slurm in python
loop python slurm
2.3 years ago by geizetomazetto • 0
0
votes
4
replies
2.7k
views
Change lines in a file within a loop in Python
loop python replace
updated 2.3 years ago by 55k • written 2.4 years ago by ▴ 60
6
votes
7
replies
3.0k
views
STAR alignment in a full directory
STAR loop
updated 2.4 years ago by ★ 4.4k • written 3.2 years ago by ▴ 30
0
votes
2
replies
850
views
renaming files and including folder/directory name in it
rename loop mv
2.4 years ago by arshad1292 ▴ 110
2
votes
1
reply
605
views
Merge/Join one data frame (X) to multiple data frames separately
join loop merge dataframe
updated 2.4 years ago by 13k • written 2.4 years ago by ▴ 70
1
vote
3
replies
1.3k
views
Loop to merge csv files
loop csv bash
updated 2.5 years ago by 44k • written 2.6 years ago by ▴ 20
11
votes
13
replies
3.4k
views
Loop for removing the complete missing rows in a n number of groups of a dataframe in R
data-frame proteomics_data loop missing_value R
2.6 years ago by KABILAN ▴ 130
0
votes
0
replies
654
views
Hi-C data analysis (Loop and domain calling)
calling and Hi-C HOMER domain Loop
2.7 years ago by arsala521 ▴ 60
2
votes
2
replies
737
views
I need to perform a sum with values from several outputs of a program
loop
2.7 years ago by pavelasquezv ▴ 50
9
votes
2
replies
933
views
How to achieve dislocation comparison, filtering and fusion of adjacent rows in a data table in R
r matrix comparison filtering loop
2.7 years ago by Chilly ★ 1.3k
19
votes
8
replies
1.9k
views
How to use R's loop to get the part of the aggregate matrix other than the many subset matrices?
aggregate r matrix loop subset
2.7 years ago by Chilly ★ 1.3k
0
votes
7
replies
1.7k
views
Basic python loop for paired fastq files
python loop
updated 2.8 years ago by 44k • written 2.8 years ago by • 0
0
votes
4
replies
1.4k
views
for loop with basename created one merged sam file instead of multiple separate sam files
bash loop bowtie2
updated 2.9 years ago by 22k • written 2.9 years ago by ▴ 30
1
vote
5
replies
1.0k
views
Bash loop one liner
liner loop centrifuge bash
updated 2.9 years ago by 6.2k • written 2.9 years ago by ▴ 10
3
votes
4
replies
1.3k
views
Loop through columns to generate PCA from DESeq2 data
pca ggplot2 deseq2 loop
updated 2.9 years ago by ★ 2.0k • written 3.0 years ago by ▴ 30
3
votes
2
replies
1.5k
views
How to apply enrichGO over a list
enrichGO clusterprofiler loop R
3.0 years ago by barix ▴ 20
1
vote
3
replies
883
views
Merge two .fastq files from two different lane
loop NGS merge fastq cat
updated 3.1 years ago by 149k • written 3.1 years ago by ▴ 310
1
vote
10
replies
3.5k
views
How to extract specific lines from a GTF file?
command-line grep loop
updated 3.1 years ago by 9.1k • written 3.1 years ago by ▴ 90
5
votes
11
replies
2.6k
views
How to apply lapply function and loop function at the same time
loop lappy Plink
3.1 years ago by Phylicia ▴ 10
2
votes
3
replies
1.6k
views
sam to bam then delete sam file
samtobam loop
updated 3.2 years ago by 11k • written 3.2 years ago by • 0
0
votes
4
replies
1.4k
views
Bash loop, count for Chromopainter script
script chromopainter bash loop
3.3 years ago by GIACOMO FRANCESCO • 0
2
votes
2
replies
1.1k
views
Snakemake pipeline with Gatk GermlineCNVCaller in Case mode
snakemake gatk cnv loop
3.3 years ago by slowbromain • 0
7
votes
5
replies
2.5k
views
Help understanding "sed" command in a loop
sed loop
updated 3.3 years ago by ★ 4.5k • written 3.3 years ago by ▴ 50
3
votes
3
replies
1.2k
views
Trying to trim last bp of several samples with BBduk at once
parameters BBduk loop bash
updated 3.4 years ago by 149k • written 3.4 years ago by • 0
5
votes
3
replies
1.8k
views
bioawk looping to retrieve fasta sequences by seq ID pattern
regex fasta bioawk loop
updated 3.7 years ago by 87k • written 3.7 years ago by ▴ 20
2
votes
1
reply
1.2k
views
Find and replace the RNAME field in BAM/SAM file
samtools bam loop sed sam
updated 3.8 years ago by 149k • written 3.8 years ago by ▴ 210
2
votes
6
replies
3.7k
views
for loop to filter dataframe based on conditions
r loop filter
3.8 years ago by katinstack • 0
7
votes
6
replies
2.1k
views
nohup with while loop
bash loop SRAtoolkit
4.0 years ago by pt.taklifi ▴ 60
3
votes
3
replies
2.0k
views
Help with parallelization and loop cutadapt
bash cutadapt loop
updated 4.2 years ago by ★ 2.1k • written 4.2 years ago by ▴ 30
1
vote
3
replies
1.1k
views
TSV fie to dataframe R for Anova
tsv dataframe r anova loop
4.2 years ago by kbaitsi • 0
3
votes
3
replies
1.0k
views
Error: object not found - Second loop
loop r
updated 4.2 years ago by ★ 4.8k • written 4.2 years ago by • 0
4
votes
7
replies
1.4k
views
problem with a for loop
linux shell loop
updated 4.2 years ago by 20 • written 4.3 years ago by ▴ 350
1
vote
2
replies
1.6k
views
Multiple plots using for loops in R
RNA-Seq R ggplot loop
updated 4.3 years ago by 4.1k • written 4.3 years ago by ▴ 390
7
votes
6
replies
1.5k
views
Looping over list in R
RNA-Seq Loop List R
updated 2.7 years ago by ▴ 10 • written 4.3 years ago by ▴ 390
0
votes
2
replies
4.3k
views
bash loop to python loop for google colabs
python loop kallisto colabs
updated 3.4 years ago by • 0 • written 4.3 years ago by • 0
1
vote
6
replies
1.4k
views
R loop using PLINK keeps stalling
R PLINK Loop
4.3 years ago by keeley.brookes • 0
5
votes
7
replies
1.4k
views
Replace FASTA file headers
fasta FASTA sed loop
updated 4.3 years ago by 22k • written 4.3 years ago by ▴ 210
5
votes
8
replies
4.5k
views
How do I use bash loop to map with Salmon on files in multiple folders
RNA-Seq mapping bash loop
updated 4.6 years ago by ★ 4.5k • written 4.6 years ago by ▴ 80
0
votes
1
reply
624
views
Problem with a function iterating over a matrix in R
R Error Loop Iteration
4.8 years ago by Pia ▴ 10
3
votes
9
replies
4.1k
views
If loop in snakemake
shell snakemake if else loop
4.9 years ago by mrmrwinter ▴ 30
2
votes
4
replies
2.5k
views
For loop to multiple fasta files using TrimAL
trimal loop sequences
updated 5.1 years ago by 149k • written 5.1 years ago by • 0
1
vote
15
replies
1.7k
views
Create txt file in a for loop
bash loop linux
updated 5.1 years ago by ▴ 140 • written 5.1 years ago by ▴ 50
50 results • Page 1 of 1
Recent Votes
Comment: Differential Expression and absolute expression
Is there a tool or method for phasing a VCF based on an already phased BAM?
A: FindConservedMarkers vs FindMarkers vs FindAllMarkers Seurat
Answer: Differential Expression and absolute expression
Comment: circos ignoring the ticks and plots
Answer: Split genotypes in VCF file
C: Plotting numbers of features in EBImage in R
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Recent Replies
Comment: Unusual File Count in 10x scMultiome Data for Cell Ranger ARC Processing by Wu-Sheng Zhang • 0
Hi @genomax , thank you very much for your help! I go through that page but still a little confused. 10x scMultiomics data would store scAT…
Comment: multiBamSummary by JC 13k
check https://broadinstitute.github.io/picard/explain-flags.html to choose a proper flag
Answer: multiBamSummary by JC 13k
Yes, `--samFlagExclude 16` will exclude reads in the reverse strand, you need `--samFlagInclude 16` (primary hits, reverse strand) or some …
Answer: Mapping ~100-300bp Sequences to Metagenome-Assembled Genomes by Mensur Dlakic ★ 29k
While I use Bowtie2, there is not a strong argument for it versus other genome aligners. I guess it is because I found a pipeline back in t…
Comment: How to convert CIGAR string to VCF? by cmdcolin ★ 4.1k
i think this is a good exercise (I wrote a quick code that I have used for cigar parsing in javascript https://cmdcolin.github.io/posts/202…
Comment: How to display a VCF/BCF file or stream as a paginated table in a python web fra by Jeremy Leipzig 23k
seqr now fully supports Hail but apparently there are some issues that will force yet another switch https://github.com/broadinstitute/seqr…
Answer: How to convert CIGAR string to VCF? by Pierre Lindenbaum 165k
pseudo code: refpos1 = <something-clipped-start> readpos0= 0; for(CigarElement ce: cigar) { char co = ce.getOpera…
Comment: Split genotypes in VCF file by Biomonika (Noolean) 3.2k
vt decompose did the trick for me, followed by the filtering for 10th and 11th column. Thanks!
Comment: Extract FUngal mRNA from RNAseq Data by GenoMax 149k
Looks good to me.
Comment: CLI Downloading from Human Microbiome Project Given Login + contact failure by Arup Ghosh 3.3k
Try the [HMP client][1] to download files from their [new portal][2]. [1]: https://github.com/IGS/portal_client [2]: https://portal.h…
Comment: Extract FUngal mRNA from RNAseq Data by SomeOne ▴ 170
i used the following command. Kindly let me know if i missed something or if it is now correct ``` bbsplit.sh ref=human_GRCh38.p14_genomic…
Comment: Gini Coefficient and Lorenz curve to measure uniformity of coverage by abascalfederico ★ 1.2k
Thank you! I finally used some code from my supervisor for the Lorenz curves, it's relatively easy, and DescTools::Gini to compute the gini…
Comment: Why do people say it doesn't matter whether you run unassembled or assembled rea by dthorbur ★ 2.8k
I'm not all that familiar with your field of research, but it would seem counterproductive to try and assemble reads of a microbial communi…
Comment: Extract FUngal mRNA from RNAseq Data by GenoMax 149k
It is worth trying. You will know reads that map to the fungal reference (even though fragmented) definitely belong there. You could also…
Comment: Extract FUngal mRNA from RNAseq Data by SomeOne ▴ 170
unfortunatly there is no chromosoem level reference genome available. But there are some genome assemblies available at scaffold or contig …
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