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363 results • Page
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Filtering for tag:
Linux
•
reset
3
votes
3
replies
147
views
Simulate 100 Reads from .fastq file | FASTQC
FASTQC
Linux
fastq
Analysis
8 days ago by
Daniel Bell
▴ 10
3
votes
7
replies
169
views
bash: sudo: command not found | ea-utils installation [CLOSED]
fastq
ea-utils
reads
bash
linux
8 days ago by
Daniel Bell
▴ 10
0
votes
2
replies
128
views
IF statement (in linux script) to merge Fastq files with similar (but not the same) names
unix
script
ifstatement
linux
fastq
updated 11 days ago by
cpad0112
15k • written 11 days ago by
endretoth
▴ 20
1
vote
2
replies
338
views
remote command line BLAST job ends in CPU error and gives MBEDTLS version mismatch
blastn
mbedtls
blast
linux
blast+
14 days ago by
janneken0210
• 0
4
votes
2
replies
904
views
Tutorial:
*FREE course* Bioinformatics for Biologists: An Introduction to Linux, Bash Scripting, and R
R
linux
bioinformatics
Tutorial
updated 27 days ago by
jessicapnoya
• 0 • written 9 weeks ago by
giessen_garten
▴ 40
3
votes
4
replies
154
views
Unused command line option: --make-just-fam
plink
GWAS
linux
updated 4 weeks ago by
davidenoma
▴ 50 • written 4 weeks ago by
suraj.adewale1
• 0
4
votes
4
replies
226
views
How to download multiple fasta files from NCBI in linux command line?
fasta
linux
command line
NCBI
updated 6 weeks ago by
Mensur Dlakic
★ 10k • written 6 weeks ago by
arriyaz.nstu
▴ 10
6
votes
6
replies
145
views
gzip: uniprot_sprot_human.dat.gz: not in gzip format
gunzip
error
linux
ubuntu
unzip
7 weeks ago by
Sashinika
• 0
1
vote
2
replies
170
views
Proper script to automate WGS analysis, typically bcftools
WGS
bcftools
linux
automation
8 weeks ago by
FL512
• 0
0
votes
1
reply
172
views
run-bwamem from BWAKIT does not work
Mapping
sequencing
next-gen
alignment
linux
updated 9 weeks ago by
Biostar
20 • written 3 months ago by
laura.zalba
• 0
0
votes
2
replies
152
views
Running Hyphy Batch File
Hyphy
Leisr
Batch File
linux
9 weeks ago by
sadstudent
• 0
0
votes
2
replies
235
views
How to run different fasta files in a same process with its output respective
bash
sequence
linux
9 weeks ago by
diego1530
▴ 40
3
votes
4
replies
170
views
Remove Extra Info From Fasta Header
fasta
RNA-Seq
sed
awk
linux
updated 9 weeks ago by
GenoMax
99k • written 9 weeks ago by
kbeavers97
• 0
3
votes
0
replies
191
views
News:
Online training - Unix and shell scripting for bioinformatics
Unix
Bioinformatics
scripting
Linux
News
10 weeks ago by
carlopecoraro2
★ 2.0k
5
votes
5
replies
230
views
how to unique a file row-wise?
awk
perl
sed
linux
updated 11 weeks ago by
dare_devil
★ 1.4k • written 11 weeks ago by
sharmatina189059
▴ 40
1
vote
5
replies
159
views
Error in opening fastq.gz file
Fastq.gz
linux
flexbar adapter atarimming
updated 3 months ago by
Ram
32k • written 3 months ago by
anthonyimhez
▴ 20
4
votes
2
replies
181
views
How to apply CUTADAPT on multiple fastq files using linux?
cutadapt
RNA-Seq
R
linux
conda
updated 3 months ago by
Pierre Lindenbaum
135k • written 3 months ago by
MatStat
▴ 140
2
votes
5
replies
214
views
How to convert columns to rows(seperated by comma) in Python(or R,linux)
R
python
linux
sequencing
seq
updated 3 months ago by
Mensur Dlakic
★ 10k • written 3 months ago by
szp770
• 0
0
votes
12
replies
283
views
how to combine two bed files using the same ID information
bed
linux
shell
python
updated 3 months ago by
Alex Reynolds
32k • written 3 months ago by
szp770
• 0
0
votes
0
replies
327
views
Filter max-missing multiple time removes more SNPs
SNP
filtering
vcftools
linux
sequencing
3 months ago by
QPaps04
▴ 30
2
votes
2
replies
1.9k
views
about Grep the complete sequences containing a specific motif in a fasta file
sequence
grep
fasta
linux
updated 3 months ago by
Biostar
20 • written 3.5 years ago by
taojincs
▴ 50
2
votes
6
replies
2.0k
views
Forum:
RIP CentOS, CentOS 8 to be EOL'd in 2021
distro
linux
os
centos
Forum
4 months ago by
5heikki
9.6k
0
votes
3
replies
187
views
Linux Path query
linux
4 months ago by
Bioinformatician_in_trouble
▴ 30
0
votes
0
replies
173
views
fatalx: OOPS indiv file has changed since genotype file was created Aborted (core dumped) problem in linux
linux
admixtools
convert
updated 4 months ago by
GenoMax
99k • written 4 months ago by
tacidilceren
• 0
3
votes
5
replies
168
views
Blast job never stops
blast
linux
updated 4 months ago by
Mensur Dlakic
★ 10k • written 4 months ago by
langziv
• 0
3
votes
9
replies
279
views
Create files in multiple directories via for loop
shell
linux
4 months ago by
vinayjrao
▴ 200
4
votes
7
replies
256
views
problem with a for loop
linux
shell
loop
updated 4 months ago by
Biostar
20 • written 5 months ago by
gubrins
▴ 70
1
vote
3
replies
253
views
Converting tsv into bam file
genome
sequencing
R
linux
updated 4 months ago by
swbarnes2
9.7k • written 4 months ago by
vinayjrao
▴ 200
0
votes
1
reply
138
views
Tools to find similarity and identity via terminal or ubuntu
sequencing
genome
alignment
bash
linux
4 months ago by
USER
• 0
1
vote
3
replies
280
views
How to extract required lines of particular chromosome from a gtf file?
RNA-Seq
gtf
linux
command
updated 5 months ago by
Ram
32k • written 5 months ago by
Biologist
▴ 200
3
votes
6
replies
269
views
filtering column based on column header from a file
bash
linux
R
updated 5 months ago by
Sam
★ 3.4k • written 5 months ago by
Bioinfonext
▴ 320
4
votes
4
replies
192
views
Large file transfer
Linux
Big data
sequencing
updated 5 months ago by
Jean-Karim Heriche
24k • written 5 months ago by
philgev2
▴ 10
2
votes
11
replies
567
views
7 follow
segmentation fault in Bayenv2
linux
bayenv
segfault
SNP
software error
updated 5 months ago by
granttbillings
• 0 • written 9 months ago by
brallen
▴ 20
0
votes
2
replies
273
views
error while executing panX script (KeyError: 'db_xref').
python
biopython
linux
bioinformatics
genome
updated 6 months ago by
Biostar
20 • written 7 months ago by
Kumar
▴ 50
0
votes
5
replies
672
views
Where should I install packages on WSL
WSL
linux
htslib
6 months ago by
n.tear
▴ 30
1
vote
5
replies
254
views
how to to download a BED file from ucsc to directory using linux
ucsc
linux
6 months ago by
kimkes25
▴ 10
3
votes
4
replies
344
views
Intall MAGIC-BLAST in Ubuntu from BASH SHELL in windows powershell.
magicblast
ncbi
ubuntu
linux
powershell
6 months ago by
jjvelazcoa
• 0
0
votes
5
replies
252
views
find -exec with multiple command
linux
unix
samtools
find command
updated 6 months ago by
Biostar
20 • written 8 months ago by
endretoth
▴ 20
0
votes
2
replies
468
views
How to convert gbk file to roary tool acceptable gff3 format?
python
perl
linux
bioinformatics
bash
updated 8 days ago by
anwesh023
▴ 10 • written 7 months ago by
Kumar
▴ 50
0
votes
2
replies
248
views
How to remove a break line \n in awk when print the result
awk
bash
linux
download assembly
updated 7 months ago by
Pierre Lindenbaum
135k • written 7 months ago by
xatabadich
• 0
3
votes
5
replies
199
views
how to change column header based on the second file column
R
BASH
LINUX
UNIX
updated 7 months ago by
Pierre Lindenbaum
135k • written 7 months ago by
Bioinfonext
▴ 320
4
votes
4
replies
233
views
Downloading gene sequences for a list of genes using E-utilities
RNA-Seq
linux
ncbi
bash
genome
7 months ago by
Bioinfonext
▴ 320
2
votes
3
replies
881
views
Error in npm installation and start.
python
linux
bash
R
software error
updated 8 months ago by
h.mon
32k • written 8 months ago by
Kumar
▴ 50
6
votes
11
replies
331
views
How to extract genome files based on genome ID
linux
R
BASH
updated 8 months ago by
bas1993
▴ 40 • written 8 months ago by
Bioinfonext
▴ 320
0
votes
0
replies
174
views
How to filter microbial genome based on genome ID
bash
linux
microbial
genome
8 months ago by
Bioinfonext
▴ 320
2
votes
2
replies
416
views
RNA-seq STAR genome mapping
RNA-Seq
STAR
Linux
updated 8 months ago by
Zhilong Jia
★ 1.7k • written 8 months ago by
waaaaaa
• 0
0
votes
6
replies
357
views
Demultiplexing fastq files
R
linux
python
sequencing
updated 9 months ago by
Ram
32k • written 9 months ago by
sidrah.maryam
▴ 30
4
votes
30
replies
453
views
Script makes different file then the manual command, but the command is the same
pipeline
linux
awk
9 months ago by
stan.aanhane
▴ 30
1
vote
3
replies
214
views
Filtering 50 biggest contigs
Novo
linux
9 months ago by
stan.aanhane
▴ 30
1
vote
3
replies
283
views
Detection nucleotide changes in VCF file
Mutation
linux
VCL
next-gen
alignment
updated 9 months ago by
Pierre Lindenbaum
135k • written 9 months ago by
stan.aanhane
▴ 30
363 results • Page
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Recent Votes
A: Could you explain the difference between STAR, KALLISTO, SALMON etc. to experime
Answer: What Do You Waste Your Time On
C: What Do You Waste Your Time On
What Do You Waste Your Time On
Answer: What Do You Waste Your Time On
Answer: What Do You Waste Your Time On
Answer: Microarray Error
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Recent Replies
Comment: Using outgroup in gene family dendograms
by
Mensur Dlakic
★ 10k
> Wouldn't a gene that isn't an ABC superfamily member from some distant species suffice as an outgroup candidate here? Most definitely no…
Comment: Testing independence between 5' and 3' terminal sequences in a DNA database
by
Istvan Albert
87k
with that definition I would suspect that all of your sequences are "dependent", I would expect every functional DNA/RNA region to capture …
Comment: Taxonomy assignment of viral RNA
by
biobiu
▴ 120
Thanks! As for the blast option- (1) so do you suggest to just blast the contig against a db of viral RNAs? and (2) is there a comprehensiv…
Comment: Finding how many times a nucleotide appear in the same position
by
cpad0112
15k
#!/usr/bin/env python3 sequences = ["GAGGTAAACTCTG", "TCCGTAAGTTTTC", "CAGGTTGGAACTC", "ACAGTCAGTTCAC", "TAGGTCATTACAG", "TAGG…
Comment: Testing independence between 5' and 3' terminal sequences in a DNA database
by
Anand Rao
▴ 350
Thanks for your reply. Yes, I think I could have explained my problem much better, but rather than change my original post, I will add some…
Answer: Finding how many times a nucleotide appear in the same position
by
Dunois
▴ 600
Here's a little `python` function you can work off of: def count_quer_at_pos_in_seq(seqs, quer = "A"): #Initialize a list…
Comment: Using outgroup in gene family dendograms
by
Rogerio Ribeiro
▴ 50
Thank for the fast reponse. The ABC family is not the best example for this question indeed. The objective of my work is to find genes resp…
Answer: Taxonomy assignment of viral RNA
by
Zhilong Jia
★ 1.7k
1. Blast directly 2. [IDSeq][1], can get viral contigs and their annotation directly. [IDSeq : An open-source cloud-based pipeline and…
Comment: Finding how many times a nucleotide appear in the same position
by
hugo.avila
▴ 180
Hi, It is not a norm but it is a good practice to post an attempted resolution first and then other members try to correct it or suggest an…
Comment: What Do You Waste Your Time On
by
ponganta
▴ 150
Aye to the rushed analyses and the last-minute documentation. Horrible, but somehow it happens all the time.
Answer: What Do You Waste Your Time On
by
ponganta
▴ 150
Reinventing the wheel. Like, all the time. Why use clusterProfiler with an up-to-date GO-annotation, when you can just write your own clien…
Comment: RNAseq data analysis of pooled data
by
ponganta
▴ 150
By "pooled" data, do you mean data from tissue-specific bulk-RNAseq? Or did you pool single cell (SC) RNAseq-libraries?
Comment: RNAseq data analysis of pooled data
by
Dunois
▴ 600
What exactly do you mean by "pooled" data?
Answer: RNAseq data analysis of pooled data
by
grant.hovhannisyan
★ 2.1k
I made a tutorial last year for University students on this topic https://www.loom.com/share/a55c1dedb8e64e7cac47f6595b751de7. Let me know …
Comment: RNAseq data analysis of pooled data
by
luffy
• 0
@dunois Thank you for the tutorial, what are your thoughts for approach for pooled data? should i follow the documentation/the tutorial or …
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