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116,887 results • Page
2 of 2338
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Votes
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32
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51
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20k
views
8 follow
Getting Unmapped Reads: Comparing Fastq To Bam
fastq
samtools
bedtools
bam
updated 12.4 years ago by
brentp
24k • written 12.4 years ago by
User 9996
▴ 840
27
votes
50
replies
18k
views
7 follow
Extract fasta sequences from a large file using a list of names
fasta
updated 15 months ago by
Ram
43k • written 9.0 years ago by
fhsantanna
▴ 620
188
votes
50
replies
73k
views
41 follow
How To Remove The Same Sequences In The Fasta Files?
fasta
sequence
duplicates
updated 19 months ago by
Ram
43k • written 13.6 years ago by
Zhangleisdau
▴ 340
94
votes
50
replies
53k
views
16 follow
PCA plot from read count matrix from RNA-Seq
RNA-Seq
pca
updated 2.5 years ago by
BioNovice247
▴ 20 • written 6.5 years ago by
rachel.kubik12
▴ 220
12
votes
50
replies
4.2k
views
How can I find out the Linux version and what is the ftp command to install R and R Studio on Linux server?
R
7.2 years ago by
thomas.f.hahn2
▴ 100
22
votes
50
replies
17k
views
Why I can not install anything on R?
R
software error
5.6 years ago by
Za
▴ 140
26
votes
50
replies
14k
views
8 follow
Tool:
Retrieve a subset of FASTA from large Illumina multi-FASTA file
fasta
multi-fasta
illumina
updated 10 months ago by
Ram
43k • written 7.9 years ago by
hcwang
▴ 50
93
votes
50
replies
16k
views
17 follow
Forum:
Fda Sends A Warning Letter To 23Andme - Personal Genomics Service Marketing To Be Discontinued
personal-genomics
23andMe
updated 14 months ago by
Ram
43k • written 10.5 years ago by
Istvan Albert
100k
85
votes
49
replies
10k
views
31 follow
Which Application Is Truly Missing In Bioinformatics?
subjective
general
updated 6 months ago by
Ram
43k • written 14.1 years ago by
Jarretinha
3.4k
262
votes
48
replies
23k
views
37 follow
Forum:
Bioinformatics courses, workshops or training
Workshop
Training
Courses
updated 14 months ago by
Lars
★ 1.0k • written 9.0 years ago by
Deepak Tanwar
★ 4.2k
72
votes
48
replies
8.5k
views
18 follow
What Kind Of Bioinformatics Tutorials Would You Like To See Online?
education
updated 15 months ago by
Ram
43k • written 13.1 years ago by
User 59
13k
68
votes
48
replies
8.8k
views
16 follow
Forum:
Stranger Things: unexpected limitations of popular tools
samtools
hisat2
updated 12 months ago by
Ram
43k • written 6.8 years ago by
Istvan Albert
100k
72
votes
48
replies
18k
views
15 follow
Tutorial:
For Short Reads, Which Aligners Find All Hits Given Certain Edit Distance Threshold?
ngs
alignment
bwa
updated 14 months ago by
Ram
43k • written 11.2 years ago by
lh3
33k
90
votes
48
replies
34k
views
29 follow
Tutorial:
Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm
rna-seq
bioconductor
updated 6 months ago by
Ram
43k • written 10.6 years ago by
Irsan
★ 7.8k
131
votes
48
replies
16k
views
19 follow
Justifying Learning Linux For Bioinformatics
linux
subjective
updated 12.8 years ago by
Guangchuang Yu
★ 2.6k • written 12.8 years ago by
Eric Normandeau
11k
39
votes
48
replies
7.0k
views
CUTADAPT in windows
sequencing
updated 15 months ago by
Ram
43k • written 9.0 years ago by
zizigolu
★ 4.3k
188
votes
47
replies
2.9k
views
16 follow
Job:
Bioinformatics freelancers needed
freelancer
updated 13 months ago by
Ram
43k • written 8.1 years ago by
Bioinfexperts
▴ 190
22
votes
47
replies
5.3k
views
(solved) I couldn't reproduce the problem of max_target_seqs
blast
updated 5.1 years ago by
gb
★ 2.2k • written 5.6 years ago by
fishgolden
▴ 510
18
votes
47
replies
4.7k
views
Fastq Trimmer by pattern
fastq
trimming
reads
terminal
7.3 years ago by
dzisis1986
▴ 70
23
votes
47
replies
7.2k
views
6 follow
Dbsnp Individual Genotyping Information For Specific Snps
dbsnp
updated 13.1 years ago by
Khader Shameer
18k • written 13.1 years ago by
Andrea_Bio
★ 2.8k
176
votes
46
replies
19k
views
26 follow
Forum:
Crac: Funny And/Or Weird Names For Bioinformatics Tools
humor
5 months ago by
Istvan Albert
100k
105
votes
46
replies
13k
views
13 follow
Forum:
Why Does Biostar Cover Questions On Epigenetics, But Not Intelligent Design?
epigenetics
updated 14 months ago by
Ram
43k • written 10.7 years ago by
ugly.betty77
★ 1.1k
126
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 13 months ago by
Ram
43k • written 8.2 years ago by
Sinji
★ 3.2k
83
votes
46
replies
9.1k
views
15 follow
Tool:
ChatGPT optimized for bioinformatics questions
gpt
updated 8 weeks ago by
LauferVA
4.2k • written 11 months ago by
Sasha
▴ 840
37
votes
46
replies
7.0k
views
12 follow
Quick Programming Challenge: How Do I Calculate Reference Coverage From A Table Of Alignment Starts And Ends?
code
alignment
programming
updated 5.7 years ago by
Ram
43k • written 14.1 years ago by
Jeremy Leipzig
22k
92
votes
46
replies
12k
views
28 follow
Best Language For Introductory Programming Course From Within An Introduction Course On Bioinformatics.
programming
subjective
updated 15 months ago by
Ram
43k • written 12.8 years ago by
Andra Waagmeester
3.2k
43
votes
46
replies
4.3k
views
taking sequences of a list of miRNAs
miRNA
mirbase
sequence
gene
updated 7.6 years ago by
Ram
43k • written 7.6 years ago by
zizigolu
★ 4.3k
185
votes
45
replies
32k
views
27 follow
How To Organize A Pipeline Of Small Scripts Together?
pipeline
general
updated 6 months ago by
Ram
43k • written 14.2 years ago by
Giovanni M Dall'Olio
28k
108
votes
45
replies
86k
views
30 follow
How To Extract A Sequence From A Big (6Gb) Multifasta File ?
fasta
updated 20 months ago by
aswinssoman
▴ 70 • written 11.8 years ago by
Mchimich
▴ 320
4
votes
45
replies
7.8k
views
SAM file wrong? help with validatesamfile
EXOME
updated 13 months ago by
Ram
43k • written 7.9 years ago by
cristina_sabiers
▴ 110
237
votes
45
replies
72k
views
34 follow
What Is The Best Pipeline For Human Whole Exome Sequencing?
next-gen
sequencing
illumina
exome
human
updated 12.9 years ago by
User 9126
▴ 50 • written 14.0 years ago by
Biomed
5.0k
22
votes
45
replies
13k
views
9 follow
Tool to separate human and mouse rna seq reads
RNA-Seq
next-gen-sequencing
updated 15 months ago by
Ram
43k • written 9.0 years ago by
Ron
★ 1.2k
46
votes
44
replies
25k
views
9 follow
bash loop for alignment RNA-seq data
RNA-Seq
next-gen
alignment
updated 19 months ago by
Ram
43k • written 10.1 years ago by
Paul
★ 1.5k
130
votes
44
replies
34k
views
16 follow
Forum:
Trimming adapter sequences - is it necessary?
NGS
adapter
RNA-Seq
updated 14 months ago by
Ram
43k • written 7.7 years ago by
Lars
★ 1.0k
121
votes
44
replies
21k
views
21 follow
What Is Your Favorite Question To Ask When Interviewing Potential Bioinformaticians?
subjective
updated 15 months ago by
Ram
43k • written 13.9 years ago by
Madelaine Gogol
5.3k
155
votes
44
replies
32k
views
29 follow
Which Bioinformatic Friendly Pipeline Building Framework?
scripting
updated 22 months ago by
Ram
43k • written 10.3 years ago by
Carlos Borroto
★ 2.1k
122
votes
44
replies
11k
views
24 follow
News:
Help Make Biostar Better! Add Your Feedback, Opinions And Suggestions.
meta
biostars
updated 6 months ago by
Ram
43k • written 11.5 years ago by
Istvan Albert
100k
99
votes
44
replies
24k
views
33 follow
Best Free Text Editor For All Popular Languages (R, Python, Perl Etc..)
text
r
perl
python
updated 6.7 years ago by
grant.hovhannisyan
★ 2.6k • written 12.2 years ago by
John
★ 1.5k
196
votes
44
replies
72k
views
33 follow
Tutorial:
Analysing Microarray Data In Bioconductor
microarray-analysis
bioconductor
updated 16 months ago by
Ram
43k • written 11.6 years ago by
Obi Griffith
20k
102
votes
44
replies
9.1k
views
22 follow
What Are Numbers Every Bioinformatician Should Know?
knowledge
career
updated 14 months ago by
Ram
43k • written 10.7 years ago by
brentp
24k
21
votes
44
replies
4.4k
views
How to analyze Illumina RNASeq data
RNA-Seq
sequencing
next-gen
3.8 years ago by
Kumar
▴ 170
90
votes
44
replies
60k
views
28 follow
Tool to generate proportional Venn Diagrams?
visualization
updated 2.0 years ago by
Ram
43k • written 13.1 years ago by
Ryan D
★ 3.4k
43
votes
44
replies
6.0k
views
14 follow
Macbook M1 pro/M2 pro or Dell (with Ubuntu/other linux distribution) for bioinformatics stuff?
metagenomics
amplicon
macbook
Intel
MacOs
updated 6 months ago by
steve
★ 3.5k • written 7 months ago by
l.gallucci
▴ 10
185
votes
44
replies
83k
views
30 follow
Drawing Chromosome Ideograms With Data
ideogram
visualization
chromosome
updated 7 weeks ago by
Michael
54k • written 14.2 years ago by
Yuri
★ 1.7k
27
votes
44
replies
15k
views
How to remove contamination from the transcriptome assembly
RNA-Seq
contamination
assembly
blast
Hiseq reads
updated 21 months ago by
Ram
43k • written 8.5 years ago by
seta
★ 1.9k
16
votes
43
replies
6.8k
views
Stuck on calculating principal components
Vegan
R
software error
SNP
updated 6.5 years ago by
pfs
▴ 280 • written 6.5 years ago by
zizigolu
★ 4.3k
31
votes
43
replies
20k
views
11 follow
Volcano plot help code
R
rna-seq
updated 5.9 years ago by
jordi.planells
▴ 480 • written 6.1 years ago by
anasofiamoreira94
▴ 80
57
votes
43
replies
16k
views
8 follow
Forum:
Best RNA-Seq aligner: A comparison of mapping tools
NGS
alignment
genome
RNA-Seq
sequence
updated 14 months ago by
Ram
43k • written 5.3 years ago by
David Langenberger
11k
59
votes
43
replies
21k
views
18 follow
Tutorial:
Polish PacBio assembly with latest PacBio tools : an affordable solution for everyone
pbalign
pacbio
arrow
smrt-limk
updated 14 months ago by
Ram
43k • written 6.6 years ago by
Rox
★ 1.4k
66
votes
43
replies
27k
views
23 follow
Ngs - Huge (Fastq) File Parsing - Which Language For Good Efficiency ?
next-gen
sequencing
parsing
fastq
programming
updated 2.3 years ago by
Ram
43k • written 13.3 years ago by
toni
★ 2.2k
116,887 results • Page
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Answer: joint callset and vcf sorting, unknown TAG issue
Answer: joint callset and vcf sorting, unknown TAG issue
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Comment: How to remove multiple batch effects from RNA-seq data before limma differential
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Include confounders into the limma design. No need for upfront removal. Note that libsize is taken care of by normalizing usually. Are you …
Comment: Longest transcript variant per gene
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Thank you very much, success in your projects.
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Thanks for the input :)
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This seems to indicate that the R verison you are using (or packages it depends on) are not compatible with the R version you are using any…
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Not my area of expertise but GTEx portal seems to offer visual comparison of expression across tissues, maybe checking their pipeline could…
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> I think I am mostly struggling with what would need to be coded to my dataset here and how to run this loop on my set in general. i do…
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Pierre, I am a novice at all of this in general and I have never used Java-based programming before. I may not be able to properly wrangl…
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There have been a couple of bugs found that affect imputation accuracy, one in build-kmer-index and one in find-paths. The find-paths bug o…
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Hi, In your samtools flagstat, -o specifies the output format. This can be set to 'default', 'json', or 'tsv'. If -o is not specified , t…
Comment: Tissue-specific DEG analysis with DEseq2
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BioinfGuru
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I wrote an R package (see [rrdr.io][1], and [github][2]) some years ago to calculate tissue specificity from bulk RNAseq based on [this pap…
Comment: joint callset and vcf sorting, unknown TAG issue
by
Pierre Lindenbaum
161k
> set the Number= to 0 instead of 1; I'm not sure it's a problem. > probably I should also change the Type to Flag ah yes, my bad ! (f…
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by
GenoMax
142k
If you posted the entire command line then you did not include `-O $MAPPING/${i}.mapping_stats.txt` in that.
Comment: joint callset and vcf sorting, unknown TAG issue
by
Matteo Ungaro
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@Pierre Lindenbaum I see. I looked up and, although present, the TAG goes like this in both files: `##INFO=<ID=1000gALT,Number=0,Type=Flag,…
Comment: joint callset and vcf sorting, unknown TAG issue
by
Matteo Ungaro
▴ 100
@Pierre Lindenbaum much appreciated, thanks for the explanation and possible approaches to solve this. I'm not in the position to run `U…
Comment: Tophat multiple or unique mapping criteria
by
Ruqaiya
• 0
> The --b2-mp defines the mismatch penalty: the first number is used when the quality of the base is good, the second when it's bad. If you…
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