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Showing top results for tag: bash • reset
2
votes
4
replies
436
views
AWK for replacing the content of a column in a csv file with the content of another column from another csv WITHOUT USING THE COLUMN NUMBER
bash awk csv
updated 5 weeks ago by 145k • written 5 weeks ago by ▴ 30
3
votes
6
replies
539
views
how to effectively pipe chromap into samtools view
samtools bash pipe
6 weeks ago by Matteo Ungaro ▴ 100
3
votes
4
replies
1.7k
views
Parallel processing of bioinformatics pipeline - running deepbgc, bagel, and antismash tools on multiple samples at once to speed up run time?
bash parallel-processing deeptools
updated 7 weeks ago by ★ 4.3k • written 23 months ago by • 0
0
votes
1
reply
435
views
HLA-HD tool for genomic imputation
bash imputation genomics
updated 8 weeks ago by 44k • written 8 months ago by ▴ 10
5
votes
1
reply
394
views
First nextflow script and I'm facing alot of errors, is my approach even correct?
Conda Bash Python Groovy Nextflow
updated 10 weeks ago by ▴ 590 • written 10 weeks ago by ▴ 50
0
votes
2
replies
767
views
HLA-HD tool for genomic imputation
genomics imputation bash
updated 4 months ago by • 0 • written 8 months ago by ▴ 10
3
votes
10
replies
939
views
Piping samtools to R
R NGS bash samtools
5 months ago by noodle ▴ 590
0
votes
1
reply
344
views
How to keep only first part of the name when adding AddOrReplaceReadGroups in multiple BAM files at a time?
SLURM BASH GATK Picard
6 months ago by kabir.deb ▴ 90
4
votes
9
replies
1.8k
views
Cutadapt error: too many parameters.
cutadapt parallel bash
updated 6 months ago by 84k • written 16 months ago by ▴ 20
1
vote
0
replies
251
views
News: shournal: A Tool for Bioinformaticians to Boost Research Reproducibility
reproducability terminal bash
6 months ago by David Langenberger 11k
2
votes
7
replies
831
views
How to turn a column into a character string (to execute filterbyname.sh of the BBTools suite)
BBTools filterbyname.sh bash
updated 7 months ago by 44k • written 7 months ago by • 0
6
votes
4
replies
976
views
Creating a csv in a specific format from FASTQ file names
nf-core bash
updated 7 months ago by • 0 • written 8 months ago by • 0
1
vote
4
replies
702
views
How to replace the sequence in the genome.fasta with reverse complement in specific chromosome and location.
genome awk edditing bash python
updated 8 months ago by 145k • written 8 months ago by ▴ 50
0
votes
2
replies
1.9k
views
How to remove binary files which are installed into /usr/local/bin
file-system Linux bash
updated 8 months ago by ★ 4.3k • written 8 months ago by ▴ 30
1
vote
1
reply
448
views
Installation error of hmmer
hmmer Linux bash
updated 8 months ago by 44k • written 8 months ago by ▴ 30
0
votes
2
replies
659
views
GATK version check failed
GATK Bash Unix
updated 9 months ago by 145k • written 9 months ago by • 0
7
votes
2
replies
6.3k
views
Trimming by fastp for multiple PE fastq.gz files using shell script
shell fastp RNA-Seq bash
written 5.9 years ago by ▴ 50
5
votes
4
replies
866
views
Importing modules based on python in bash script wont work
python pipeline conda bash
updated 9 months ago by ★ 1.1k • written 9 months ago by ▴ 10
2
votes
2
replies
678
views
News: Unix and Shell Scripting for Bioinformatics course
Bash Unix Shell-Scripting
9 months ago by carlopecoraro2 ★ 2.6k
4
votes
3
replies
923
views
Running cellranger on multiple files when R1 and R2 fastqs are in multiple subfolders
singlecell cellranger bash
updated 9 months ago by 84k • written 9 months ago by ▴ 20
1
vote
2
replies
495
views
Autocompleting paths within scripts
nano vim bash remote vscode
9 months ago by DanielEB_fisk ▴ 20
5
votes
3
replies
1.4k
views
How to overlap patient VCF with ClinVar database annotation using bedtools?
bedtools bash ClinVar overlap VCF
updated 10 months ago by 44k • written 10 months ago by ▴ 10
3
votes
6
replies
927
views
FASTA File Concatenation
bash FASTA
updated 11 months ago by 44k • written 11 months ago by • 0
4
votes
2
replies
865
views
Writing a for loop with if statement to concatenate files with the same end of name in linux
shell linux bash
11 months ago by arnoldhaley3 ▴ 10
1
vote
5
replies
1.0k
views
Error: cannot open file 2 for reading From Cufflinks Version 2.2.1 When Attempting To Use CuffDiff
CuffDiff Bash Cufflinks
12 months ago by Y • 0
0
votes
0
replies
320
views
Reverse complement only sequences resulted from BLASTN minus
DNA fasta bash
updated 12 months ago by 44k • written 12 months ago by ▴ 30
0
votes
3
replies
601
views
Step 2 Error Intron Clustering For LeafCutter
Bash Leafcutter
13 months ago by Y • 0
4
votes
11
replies
2.0k
views
Check Strandedness
Check_Strandedness how_are_we_stranded_here leafcutter bash
updated 11 months ago by 20k • written 13 months ago by • 0
147
votes
33
replies
141k
views
27 follow
Useful Bash Commands To Handle Fasta Files
command-line fasta bash
updated 5 days ago by 44k • written 12.6 years ago by ★ 2.9k
1
vote
2
replies
1.3k
views
How to choose BWA-MEM2 settings
BWA-MEM2 DNA-seq bash
updated 14 months ago by 44k • written 14 months ago by ▴ 50
0
votes
4
replies
1.0k
views
calculating read depth via a for in loop over many fastq files ?
Linux R bash
14 months ago by Mohamed Samir ▴ 30
2
votes
4
replies
793
views
How to salvage incomplete PLINK .bed files?
PLINK bash
updated 14 months ago by 145k • written 14 months ago by ▴ 10
1
vote
2
replies
655
views
For loop in bash script
bash
updated 15 months ago by 44k • written 15 months ago by • 0
3
votes
4
replies
1.2k
views
Bash solution to replace part of FASTA headers witch contain matching values in another file
fasta awk bash seqkit sed
15 months ago by clmattson • 0
0
votes
4
replies
1.1k
views
How to join multiple large .tsv (> 20 GB, bed file) files by two identifier?
bash Python R bed
updated 15 months ago by 44k • written 15 months ago by ▴ 90
3
votes
2
replies
2.5k
views
Help speeding up HMMER's HMMSearch algorithm for large fasta file with GNU Parallel
protein parallel hmmer hmm bash
updated 15 months ago by 15k • written 3.1 years ago by ▴ 740
3
votes
4
replies
834
views
Need help editing text in the shell
bash shell
updated 15 months ago by 44k • written 15 months ago by ▴ 20
3
votes
5
replies
802
views
Concatenating text files based on common indices
Bash Python
updated 16 months ago by 44k • written 16 months ago by • 0
1
vote
6
replies
2.4k
views
Using entrez-direct inside a for loop in bash
NCBI bash
updated 16 months ago by 145k • written 5.6 years ago by ▴ 30
3
votes
11
replies
2.2k
views
6 follow
BLAST command line scripting
BASH
updated 16 months ago by 21k • written 16 months ago by ▴ 10
3
votes
8
replies
1.3k
views
sorting and moving a bunch of fasta files into separate folder
fasta bash
updated 17 months ago by 44k • written 18 months ago by • 0
1
vote
4
replies
1.4k
views
Creating a loop to mark duplicates using Picard
bash picard
updated 18 months ago by 44k • written 18 months ago by • 0
0
votes
2
replies
632
views
OrthoFinder problem
Sub OrthoFinder iterative processes Bash
18 months ago by HERMAN ▴ 10
3
votes
12
replies
1.6k
views
prefix extraction and preparation for mapping and variant calling
bash
updated 18 months ago by 21k • written 18 months ago by • 0
11
votes
8
replies
1.8k
views
6 follow
split fasta file to train deep learning model
fasta split bash R
updated 18 months ago by 8.6k • written 18 months ago by ▴ 90
2
votes
4
replies
1.3k
views
Trouble with transcripts_id when using how_are_we_stranded_here python package
bash sequencing RNA-seq
18 months ago by ExtentHonest56 ▴ 20
3
votes
5
replies
1.1k
views
Can someone help me with searching overlapping values between two files?
bash grep awk MATCH
updated 18 months ago by 164k • written 19 months ago by • 0
2
votes
2
replies
768
views
Using Entrez to download Supplementary files in GEO entry via command line?
bash command-line entrez
updated 19 months ago by 44k • written 19 months ago by ▴ 30
1
vote
0
replies
453
views
Default placeholder for missing fields doesn't work with block in xtract tool
bash nbci-tools xtract
19 months ago by Crunk ▴ 10
0
votes
0
replies
406
views
Gene names/ids on annotated protein files
bash Protein GFF annotation
updated 19 months ago by 145k • written 19 months ago by ▴ 50
50 results • Page 1 of 1
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Answer: Converting bam to sam using htslib C++ api
Answer: How to compile Multiz
Comment: How to compile Multiz
Alignment tool for very short reads (25bp)
Comment: How to compile Multiz
Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
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Comment: Sankey + dot plot by zx8754 12k
What is the problem, where is the code you are trying? Provide code, example data, expected output.
Answer: I have encountered some bugs in transcriptome analysis using STAR and RSEM. by Michael 55k
Something went wrong during star alignments of samples OE1_2, OE1_3, and OE_NC_1. The obvious place to look for the reason is in the Star l…
Comment: How to compile Multiz by Pierre Lindenbaum 164k
> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
Comment: How to compile Multiz by Santex • 0
I'm sorry. I post a new question.
Comment: NeuronChat: identifyCommunicationPatterns_Neuron() error by sooni ▴ 20
I solved the problem by installing `NMF` package.
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM. by GenoMax 145k
Can you check using `featureCounts` to make sure things look reasonable with alignments? You could also use `salmon` to do transcript quant…
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM. by GenoMax 145k
Since we don't have access to your data we can't comment. Check the integrity of your input data files. Validate the files if you are not s…
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM. by GenoMax 145k
https://www.biostars.org/u/145859/ : Use `ADD REPLY/ADD COMMENT` to add additional information to existing threads. `ADD YOUR ANSWER` is me…
Comment: How to compile Multiz by GenoMax 145k
Please do not ask questions unrelated to the original post in this thread. Post a new question.
Comment: How to compile Multiz by Santex • 0
I could install multiz from it! Thank you very much. Please help me out with the problem below. I run multiz like below. (myenv) tak…
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM. by Pallondyle • 0
One of them looks okay, but I don't quite believe it. ```R > table(df$`intermediate_data.OE1_1_.genes.results`==0) FALSE TRUE 21200 2…
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM. by Pallondyle • 0
It seems that the files that generated the results also have significant issues. Except for one sample, all other samples only have over 20…
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM. by Pallondyle • 0
Their .fq files all look similar, should I rerun these programs?
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM. by GenoMax 145k
> Cannot open intermediate_data/OE_NC_2_.temp/OE_NC_2__alignable_1.fq! It may not exist. Looks like you are missing some files. BTW this …
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM. by Pallondyle • 0
The most torturous thing is that some groups did indeed generate results. ``` ls intermediate_data KO1_1_.stat KO1_3_.isoforms…
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