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1,000 results • Page
1 of 20
Sort: Views
Rank
Views
Votes
Replies
226
votes
39
replies
287k
views
33 follow
Gene Id Conversion Tool
david
updated 5 months ago by
Ram
43k • written 14.4 years ago by
Renee
▴ 620
331
votes
92
replies
237k
views
58 follow
Tools To Calculate Average Coverage For A Bam File?
coverage
bam
sequencing
updated 7 months ago by
kalavattam
▴ 190 • written 13.2 years ago by
Biomed
4.9k
120
votes
31
replies
197k
views
17 follow
Correct Way To Parse A Fasta File In Python
python
fasta
updated 4 months ago by
Ram
43k • written 14.0 years ago by
Eric Normandeau
11k
62
votes
14
replies
195k
views
9 follow
How To Deal With Duplicate Row Names Error In R
r
updated 11 months ago by
zx8754
11k • written 11.1 years ago by
Diana
▴ 910
124
votes
13
replies
173k
views
13 follow
How Can I Convert Bam To Sam?
bam
next-gen-sequencing
sam
updated 6 months ago by
Ram
43k • written 13.7 years ago by
Biomed
4.9k
143
votes
14
replies
169k
views
16 follow
What Is The Sequencing 'Depth' ?
next-gen
sequencing
updated 4 months ago by
Ram
43k • written 14.0 years ago by
Pierre Lindenbaum
160k
98
votes
39
replies
155k
views
19 follow
Extract Reads From A Bam File That Fall Within A Given Region
bam
updated 11 months ago by
Dan
▴ 180 • written 11.7 years ago by
abi
▴ 390
231
votes
38
replies
145k
views
29 follow
Tool:
Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
ensembl
genome-coordinates
liftover
updated 9 months ago by
Ram
43k • written 11.1 years ago by
Malachi Griffith
19k
362
votes
82
replies
143k
views
35 follow
Tool:
Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
parallel
next-gen
ngs
updated 2 days ago by
jena
▴ 290 • written 11.1 years ago by
ole.tange
★ 4.4k
793
votes
167
replies
139k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 9 weeks ago by
Biostar
2.6k • written 7.3 years ago by
Istvan Albert
100k
147
votes
31
replies
136k
views
26 follow
Useful Bash Commands To Handle Fasta Files
command-line
fasta
bash
updated 8 months ago by
Ram
43k • written 12.1 years ago by
Anima Mundi
★ 2.9k
68
votes
18
replies
128k
views
14 follow
from .BAM to .BAI using samtools
next-gen-sequencing
samtools
updated 8 weeks ago by
Pierre Lindenbaum
160k • written 9.5 years ago by
Kizuna
▴ 870
76
votes
26
replies
118k
views
15 follow
How to count fastq reads
sequence
next-gen
fastq
reads
updated 4 months ago by
cschu181
★ 2.8k • written 8.9 years ago by
Chenglin
▴ 260
103
votes
34
replies
112k
views
23 follow
How To Split A Bam File By Chromosome
bam
updated 11 weeks ago by
Ram
43k • written 11.8 years ago by
GPR
▴ 390
105
votes
15
replies
111k
views
16 follow
Convertion Of Gff3 To Gtf
gtf
gff
updated 8 days ago by
xiaoleiusc
▴ 140 • written 11.8 years ago by
GouthamAtla
12k
124
votes
56
replies
102k
views
24 follow
How to plot coverage and depth statistics of a bam file
bam
coverage
depth
next-gen-sequencing
updated 5 months ago by
William
▴ 30 • written 9.8 years ago by
kay
▴ 370
170
votes
41
replies
97k
views
27 follow
Multiline Fasta To Single Line Fasta
fasta
updated 6 months ago by
Ram
43k • written 12.8 years ago by
Palu
▴ 250
239
votes
176
replies
94k
views
73 follow
Tutorial:
Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq
Survival
TCGA
updated 10 months ago by
Ram
43k • written 8.7 years ago by
TriS
★ 4.7k
105
votes
31
replies
93k
views
18 follow
Best Way To Merge A Many Thousand Small Bam Files Into One Big Bam File?
bam
picard
samtools
merge
updated 3 months ago by
mmfansler
▴ 450 • written 12.7 years ago by
2184687-1231-83-
★ 5.1k
97
votes
19
replies
93k
views
12 follow
How To Get The Sequence Of A Genomic Region From Ucsc?
ucsc
fasta
sequence
updated 5 months ago by
Ram
43k • written 14.1 years ago by
Giovanni M Dall'Olio
28k
93
votes
23
replies
90k
views
15 follow
Tutorial:
How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools
samtools
htslib
updated 9 weeks ago by
clara.apicella
• 0 • written 5.7 years ago by
otwtgin2010
▴ 610
103
votes
27
replies
88k
views
21 follow
Extract Sub-Set Of Regions From Vcf File
vcf
tabix
genome
filter
updated 10 months ago by
NIRJHAR
• 0 • written 11.8 years ago by
Rubal7
▴ 830
163
votes
64
replies
86k
views
39 follow
Selecting Random Pairs From Fastq?
random
fastq
illumina
sequence
updated 8 weeks ago by
Ram
43k • written 13.0 years ago by
Ketil
4.1k
19
votes
14
replies
85k
views
10 follow
BLAST Database error: No alias or index file found for nucleotide database
blast
blastn
sift
makeblastdb
updated 5 months ago by
Ken
• 0 • written 9.4 years ago by
arronslacey
▴ 320
185
votes
44
replies
83k
views
30 follow
Drawing Chromosome Ideograms With Data
ideogram
visualization
chromosome
updated 8 days ago by
Michael
54k • written 14.0 years ago by
Yuri
★ 1.7k
363
votes
58
replies
69k
views
44 follow
Forum:
Recommend Your Favorite Bioinformatics Books
education
books
updated 5 months ago by
Ram
43k • written 14.1 years ago by
Istvan Albert
100k
137
votes
22
replies
64k
views
15 follow
How do I explain the difference between edgeR, LIMMA, DESeq etc. to experimental Biologist/non-bioinformatician
gene
LIMMA
edgeR
updated 9 months ago by
Kevin Blighe
87k • written 6.4 years ago by
Mike
★ 1.9k
328
votes
54
replies
63k
views
45 follow
What Tools/Libraries Do You Use To Visualize Genomic Feature Data?
genome
visualization
updated 4 months ago by
Ram
43k • written 14.0 years ago by
brentp
24k
159
votes
24
replies
62k
views
19 follow
Recommended Tools For Alternative Splicing Detection From Rna-Seq Data
alternative-splicing
splicing
rna-seq
updated 9 months ago by
Ram
43k • written 11.1 years ago by
Nicolas Rosewick
10k
102
votes
30
replies
61k
views
25 follow
Tools To Find Gene Ontology Term Enrichment
gene
enrichment
updated 5 months ago by
Ram
43k • written 14.1 years ago by
Biostar User
★ 1.0k
164
votes
70
replies
60k
views
34 follow
How To Efficiently Parse A Huge Fastq File?
fastq
next-gen-sequencing
updated 5 hours ago by
Ram
43k • written 12.7 years ago by
Panos
★ 1.8k
93
votes
19
replies
59k
views
18 follow
What Is A Good Phylogenetic Tree Display Program For Large Data Sets?
phylogenetics-tree
updated 9 months ago by
Ram
43k • written 13.6 years ago by
Niek De Klein
★ 2.6k
17
votes
6
replies
59k
views
Turn Off Blast Search On Reverse Complement Strand In Blastn
blast
sequence
updated 5 months ago by
Ram
43k • written 14.1 years ago by
Zhaorong
★ 1.4k
52
votes
8
replies
59k
views
7 follow
Subsampling Bam File With Samtools
bam
samtools
updated 11 weeks ago by
giulia.trauzzi
▴ 10 • written 10.7 years ago by
madbessoul
▴ 250
1.2k
votes
206
replies
58k
views
108 follow
Forum:
What Are The Most Common Stupid Mistakes In Bioinformatics?
software
updated 10 months ago by
Raony Guimarães
★ 1.4k • written 13.0 years ago by
Jeremy Leipzig
22k
44
votes
9
replies
57k
views
FindConservedMarkers vs FindMarkers vs FindAllMarkers Seurat
next-gen
RNA-Seq
single-cell
R
updated 8 months ago by
camillab.
▴ 160 • written 4.3 years ago by
Payal
▴ 160
28
votes
22
replies
57k
views
11 follow
How To Convert List Of Entrez Ids Into Gene Name
r
genomics
entrez
updated 9 months ago by
cwang3444
• 0 • written 10.9 years ago by
grosy
▴ 90
50
votes
13
replies
56k
views
13 follow
Calculating TPM from featureCounts output
RNA-Seq
updated 6 months ago by
camillab.
▴ 160 • written 8.2 years ago by
nash.claire
▴ 490
61
votes
23
replies
56k
views
15 follow
How Can I Know The Length Of Mapped Reads From Bam File?
bam
mapping
updated 4 months ago by
Lluís R.
★ 1.2k • written 11.1 years ago by
Jordan
★ 1.3k
0
votes
3
replies
52k
views
Tutorial:
Installation VMD on LINUX_64
gromacs
VMD
updated 11 months ago by
Ram
43k • written 7.8 years ago by
Hassan Rasouli
▴ 10
66
votes
19
replies
50k
views
17 follow
Tool To Find Out If Fastq Is In Sanger Or Phred64 Encoding?
fastq
updated 9 months ago by
Ram
43k • written 11.1 years ago by
14134125465346445
★ 3.6k
149
votes
70
replies
50k
views
20 follow
Tutorial:
Network plot from expression data in R using igraph
microarray
RNA-Seq
R
network
updated 7 months ago by
Raheleh
▴ 260 • written 6.4 years ago by
Kevin Blighe
87k
125
votes
46
replies
50k
views
21 follow
Forum:
Visualization of ChIP-seq data using Heatmaps (Updated: 06/10/16)
visualization
ChIP-Seq
homer
ngsplot
deeptools
updated 11 months ago by
Ram
43k • written 8.1 years ago by
Sinji
★ 3.2k
56
votes
52
replies
49k
views
12 follow
Tool:
Gene Set Clustering based on Functional annotation (GeneSCF)
geneSCF
Gene-Clustering
updated 9 months ago by
Ram
43k • written 9.6 years ago by
EagleEye
7.5k
52
votes
21
replies
49k
views
11 follow
Fastq Splitter For Paired End Reads
rna
updated 9 months ago by
Ram
43k • written 12.0 years ago by
Geparada
★ 1.5k
66
votes
23
replies
48k
views
8 follow
extract dendrogram cluster from pheatmap
R
updated 11 days ago by
Getnet Tesfaw
• 0 • written 6.3 years ago by
1769mkc
★ 1.2k
71
votes
15
replies
48k
views
10 follow
Definition of minor and major allele and connection with risk, effect, wildtype and reference allele
risk
minor
major
reference
alleles
written 5.9 years ago by
m98
▴ 420
3
votes
5
replies
47k
views
Convert text file to VCF file ?
vcf
updated 9 months ago by
Ram
43k • written 9.1 years ago by
CrazyB
▴ 280
34
votes
19
replies
47k
views
11 follow
Convert Refseq Id To Gene Name
refseq
gene
updated 8 months ago by
Ram
43k • written 10.8 years ago by
hicsuntdrac0nis
▴ 250
9
votes
12
replies
45k
views
8 follow
Tools to view fastq file
fastq
updated 9 months ago by
Ram
43k • written 7.9 years ago by
Roden Luo
▴ 40
1,000 results • Page
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Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
GenoMax
140k
The question you should be looking into is why the Q scores are dropping there? Are there `N` calls indicating some issue with that cycle?
Comment: Error in openning FastQC
by
GenoMax
140k
What is `ctrl+c ctrl+v`? You may actually be killing the running fastqc process. If you run `fastqc` interactively (like what was shown ab…
Comment: F*up Night style events for Bioinformatics ? Comment if you're interested!
by
Dave Carlson
★ 1.7k
Ugh. I've definitely done this one before as well. And was none too happy about it.
Comment: Error in openning FastQC
by
friszd
• 0
fastqc -o output.html input.fastq ctrl+c ctrl+v
Comment: Error running local blastn in R using system2
by
GenoMax
140k
What do you see if you `cat nt_euk.nal`? Do the number of pieces mentioned in that file match with what you locally have?
Comment: Low number of both surviving reads after trimming
by
GenoMax
140k
It is your data and if you want to do that it is up to you. You may be throwing away essentially good data (you should remove the nextera s…
Comment: F*up Night style events for Bioinformatics ? Comment if you're interested!
by
Istvan Albert
100k
Some things never change ... the most common mistake is still the one on top there
Comment: Low number of both surviving reads after trimming
by
Ram
43k
I see that the code content was not added again, just the formatting modified. The output is still mangled. Compare it to the output you se…
Answer: F*up Night style events for Bioinformatics ? Comment if you're interested!
by
Mensur Dlakic
★ 26k
I was trying to avoid re-living traumatic events, but here goes. This is an attempt to delete all the files with a certain extension but in…
Comment: Low number of both surviving reads after trimming
by
Jay
• 0
Thank you for your response. There was no particular reason of `LEADING:20 and TRAILING:20`, but I used the same parameters as I had used …
Comment: Low number of both surviving reads after trimming
by
GenoMax
140k
A significant fraction of your reads appear to have the nextera sequence, that combined to this directive `LEADING:20` (do you have a reaso…
Comment: Low number of both surviving reads after trimming
by
Jay
• 0
Here is my fastqc, especially adapter content graph, before trimming(R1 and R2): ![enter image description here][1] And this after trimm…
Comment: Low number of both surviving reads after trimming
by
Jay
• 0
Thanks, I modified.
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by
Pierre Lindenbaum
160k
11 years ago: https://www.biostars.org/p/7126/
Comment: F*up Night style events for Bioinformatics ? Comment if you're interested!
by
Dave Carlson
★ 1.7k
haha yes exactly! After the first or second ruined fasta, I started "catting" all fasta files and piping to other commands, just to reduce …
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