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Showing top results for tag: Linux • reset
1
vote
5
replies
287
views
  Amount of unique variants in VCF with linux terminal
variants unique VCF linux
updated 20 hours ago by ▴ 60 • written 5 days ago by • 0
4
votes
4
replies
203
views
  How to get number of characters (nucleotides) in fasta file
count fasta linux characters commands
updated 2 days ago by 5.9k • written 3 days ago by ▴ 20
0
votes
0
replies
96
views
  How to update phenotype in .fam file.
GWAS plink linux unix
6 days ago by geno89 ▴ 10
1
vote
1
reply
105
views
  Salmon quant produced an error
Salmon Linux
updated 10 days ago by 50k • written 10 days ago by ▴ 10
3
votes
2
replies
130
views
  For loop to parallel run commands
Unix bash Linux
11 days ago by endretoth ▴ 20
2
votes
12
replies
868
views
9 follow
  segmentation fault in Bayenv2
linux bayenv segfault SNP software error
updated 13 days ago by • 0 • written 12 months ago by ▴ 20
1
vote
10
replies
361
views
  Sorting of a bam file takes toooo long time
file linux bam
updated 14 days ago by 34k • written 15 days ago by ▴ 10
0
votes
3
replies
170
views
  SOAPaligner- 2bwt-builder segmentation fault
soapaligner c linux
updated 48 minutes ago by 34k • written 18 days ago by • 0
0
votes
1
reply
77
views
  Extract co-ordinate for iCLIP data?
sequencing linux RNA
updated 19 days ago by 88k • written 19 days ago by ▴ 30
0
votes
2
replies
121
views
  RNA-seq different reads numbers of two samples is trouble?
RNA-Seq R seq python linux
updated 20 days ago by ▴ 990 • written 20 days ago by ▴ 10
3
votes
0
replies
119
views
News:  Linux for Biologists e-book is free for one more week
python conda virtual-machine linux galaxy
18 days ago by Vimalkumar Velayudhan (Vimal) ▴ 250
0
votes
7
replies
296
views
  Changing sample name in multiple VCF files
gatk bcftools linux vcf
updated 26 days ago by 74k • written 27 days ago by • 0
0
votes
5
replies
182
views
  Print rows where the columns have a specific condition
awk linux bash
updated 4 weeks ago by 16k • written 4 weeks ago by ▴ 10
7
votes
3
replies
220
views
  Why my files ended with ^M ?? (shell/bash)
shell linux cat grep bash
5 weeks ago by nlt_220593 ▴ 10
4
votes
4
replies
200
views
  Reads alignment on human and pathogen combined genome
linux STAR alignment
updated 25 days ago by 34k • written 5 weeks ago by • 0
2
votes
3
replies
712
views
  cannot import name 'gcd' from 'fractions'
ubuntu Linux python multiqc
updated 5 weeks ago by ▴ 710 • written 10 weeks ago by • 0
0
votes
1
reply
112
views
  How split regions in half to get at most 1000 bp length?
split linux bedtools R chop
updated 6 weeks ago by 136k • written 6 weeks ago by ▴ 270
1
vote
5
replies
311
views
  convert tabular data to fasta
linux forum convert fasta
6 weeks ago by zahra • 0
0
votes
0
replies
73
views
  bash question: Copy Files to New Directory Using List of File Order
loops bash cli linux command_line
6 weeks ago by Simone • 0
0
votes
4
replies
169
views
  InterProScan proxy warning
linux lookup http
6 weeks ago by Sergio • 0
4
votes
4
replies
177
views
  Files recognized as gzip but not compressed
Linux gzip BAM Ubuntu
6 weeks ago by beaferbl ▴ 10
2
votes
2
replies
252
views
  Remove all rows that begin with characters and keep only those that begin with numbers in Linux.
hg19 linux
updated 6 weeks ago by 32k • written 7 weeks ago by ▴ 30
5
votes
5
replies
427
views
  how to run linux code in python
shell python sh bash linux
8 weeks ago by szp770 ▴ 10
0
votes
2
replies
144
views
  Trimmomatic log file format explanation?
Linux Trimmomatic
8 weeks ago by willbrown • 0
6
votes
12
replies
821
views
7 follow
  Multiqc raises the "cannot import name 'gcd' from 'fractions'" error
multiqc linux rna-sq
updated 8 weeks ago by ▴ 710 • written 9 weeks ago by • 0
0
votes
4
replies
309
views
  sequence similarity
blast linux fasta
updated 8 weeks ago by 19k • written 8 weeks ago by • 0
3
votes
5
replies
536
views
  Intall MAGIC-BLAST in Ubuntu from BASH SHELL in windows powershell.
magicblast ncbi ubuntu linux powershell
updated 8 months ago by 102k • written 8 months ago by • 0
0
votes
2
replies
152
views
  Converting tab character file to a tab delimited file
Linux
updated 9 weeks ago by 50k • written 9 weeks ago by ▴ 20
0
votes
2
replies
232
views
  Segmentation fault (core dumped) error in MUSCLE
NGS alignment fastq linux sequence
10 weeks ago by christopherjamessteel1990 • 0
3
votes
3
replies
296
views
  Simulate 100 Reads from .fastq file | FASTQC
FASTQC Linux fastq Analysis
11 weeks ago by Daniel Bell ▴ 10
3
votes
7
replies
263
views
  bash: sudo: command not found | ea-utils installation [CLOSED]
fastq ea-utils reads bash linux
11 weeks ago by Daniel Bell ▴ 10
0
votes
2
replies
238
views
  IF statement (in linux script) to merge Fastq files with similar (but not the same) names
unix script ifstatement linux fastq
updated 11 weeks ago by 16k • written 11 weeks ago by ▴ 20
1
vote
2
replies
461
views
  remote command line BLAST job ends in CPU error and gives MBEDTLS version mismatch
blastn mbedtls blast linux blast+
12 weeks ago by janneken0210 • 0
4
votes
2
replies
1.2k
views
Tutorial:  *FREE course* Bioinformatics for Biologists: An Introduction to Linux, Bash Scripting, and R
R linux bioinformatics Tutorial
updated 3 months ago by • 0 • written 4 months ago by ▴ 40
3
votes
4
replies
228
views
  Unused command line option: --make-just-fam
plink GWAS linux
updated 3 months ago by ▴ 50 • written 3 months ago by • 0
4
votes
4
replies
360
views
  How to download multiple fasta files from NCBI in linux command line?
fasta linux command line NCBI
updated 3 months ago by ★ 11k • written 3 months ago by ▴ 10
6
votes
6
replies
220
views
  gzip: uniprot_sprot_human.dat.gz: not in gzip format
gunzip error linux ubuntu unzip
4 months ago by Sashinika • 0
1
vote
2
replies
214
views
  Proper script to automate WGS analysis, typically bcftools
WGS bcftools linux automation
4 months ago by FL512 • 0
0
votes
1
reply
213
views
  run-bwamem from BWAKIT does not work
Mapping sequencing next-gen alignment linux
updated 4 months ago by 20 • written 6 months ago by • 0
0
votes
2
replies
198
views
  Running Hyphy Batch File
Hyphy Leisr Batch File linux
4 months ago by sadstudent • 0
0
votes
2
replies
286
views
  How to run different fasta files in a same process with its output respective
bash sequence linux
4 months ago by diego1530 ▴ 40
3
votes
4
replies
222
views
  Remove Extra Info From Fasta Header
fasta RNA-Seq sed awk linux
updated 4 months ago by 102k • written 4 months ago by • 0
3
votes
0
replies
249
views
News:  Online training - Unix and shell scripting for bioinformatics
Unix Bioinformatics scripting Linux News
4 months ago by carlopecoraro2 ★ 2.0k
5
votes
5
replies
293
views
  how to unique a file row-wise?
awk perl sed linux
updated 5 months ago by ★ 1.4k • written 5 months ago by ▴ 60
1
vote
5
replies
200
views
  Error in opening fastq.gz file
Fastq.gz linux flexbar adapter atarimming
updated 5 months ago by 34k • written 5 months ago by ▴ 20
4
votes
2
replies
237
views
  How to apply CUTADAPT on multiple fastq files using linux?
cutadapt RNA-Seq R linux conda
updated 5 months ago by 136k • written 5 months ago by ▴ 140
2
votes
5
replies
348
views
  How to convert columns to rows(seperated by comma) in Python(or R,linux)
R python linux sequencing seq
updated 5 months ago by ★ 11k • written 5 months ago by ▴ 10
0
votes
12
replies
360
views
  how to combine two bed files using the same ID information
bed linux shell python
updated 5 months ago by 32k • written 5 months ago by ▴ 10
0
votes
0
replies
472
views
  Filter max-missing multiple time removes more SNPs
SNP filtering vcftools linux sequencing
6 months ago by QPaps04 ▴ 40
2
votes
2
replies
2.0k
views
  about Grep the complete sequences containing a specific motif in a fasta file
sequence grep fasta linux
updated 6 months ago by 20 • written 3.7 years ago by ▴ 50
50 results • Page 1 of 1
Recent Votes
A: Blast - Formatting Output
A: Blast - Formatting Output
Answer: Which R function can be used for intersection of genomic coordinates from one fi
Answer: Which R function can be used for intersection of genomic coordinates from one fi
Comment: Hello everyone.How can i do miRNAmeta analysis in plant?thanks alot
Answer: Which R function can be used for intersection of genomic coordinates from one fi
Answer: How to Speed Up BLASTp
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Recent Awards • All
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Recent Replies
Comment: pearson correlation between lncRNA and mRNA by MS ▴ 20
Beacause when I checked txt files are not seperated anything I leaved it empty. Actually when I check the input data in R it looks okay.
Comment: pearson correlation between lncRNA and mRNA by Ram 34k
If there are 36 columns, they must be separated by something. Why is your `sep` an empty string?
Comment: pearson correlation between lncRNA and mRNA by MS ▴ 20
Thank you for your reply. the 2 files are txt files including 36 column both of them but row numbers are different and it gives lenght of x…
Comment: extracting ensembl gene id or entrez gene id from a gene annotation file for BIN by Pancreas Pratik ▴ 300
I think you might just simply have to remove the underscores `_` You could do that manually or in terminal like so: cat yourgenes.txt…
Comment: How to Speed Up BLASTp by GenoMax 102k
> considering building a local database only including protein sequences > from viruses. I think you are best off getting the viral protei…
Comment: Adding p value to Vlnplot in Seurat by antonioggsousa ★ 2.1k
Hi @jvbeltran0122, As far as I remember by default the function `stat_compare_means()` ([link](https://rpkgs.datanovia.com/ggpubr/referen…
Comment: How to Speed Up BLASTp by twangxxx • 0
It's over two hours since I initiated a single sequence blastp against all nr databases as I mentioned in my previous reply, and It hasn't …
Comment: How to Speed Up BLASTp by h.mon 32k
You can try the variable `$PBS_NUM_PPN` (number of CPUs per node): blastp -db nr -query proteins.fa -outfmt 6 -out ./output.txt \ …
Comment: Bioinformaticist or computational biologist opportunity at Pattern Ag (CA, USA) by Danielle • 0
Thanks for the suggestion
Comment: De Novo Assembly from Oligos by GenoMax 102k
Perhaps `tadpole.sh` from [**BBMap suite**][1] may work. [**Tadpole guide**][2] is available. [1]: https://sourceforge.net/projects/…
Answer: Which R function can be used for intersection of genomic coordinates from one fi by seidel 8.0k
For R the GenomicRanges package is made for this (as mentioned by @jared.andrews07). library(GenomicRanges) library(rtracklayer…
Comment: RELATED NEIGHBOURING GENES IN A PATHWAY by Ram 34k
All caps is rude. Please edit your post title, and also add details on what you've tried so far.
Comment: FASTQC per base sequence quality by BIN • 0
Alright thanks GenoMax !
Answer: FASTQC per base sequence quality by GenoMax 102k
Because your data is of extremely good quality with Q scores > 36 (except for last bin/cycles). Normal with good libraries and current sequ…
Comment: Bioinformaticist or computational biologist opportunity in metagenomics by 4galaxy77 ▴ 730
"ML techniques such as hierarchical clustering" yikes
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