11
votes
28
replies
3.6k
views
6 follow
1
vote
2
replies
164
views
0
votes
0
replies
90
views
Tutorial:
Making LDA Score plot
6 days ago by
rohitsatyam102
▴
640
126
votes
122
replies
25k
views
23 follow
Tutorial:
Survival analysis with gene expression
updated 22 days ago by
Athanasios
•
0
•
written 3.9 years ago by
Kevin Blighe
83k
9
votes
7
replies
3.6k
views
11
votes
1
reply
1.3k
views
10
votes
6
replies
1.2k
views
79
votes
21
replies
11k
views
16 follow
Tutorial:
Gene Set Enrichment Analysis
updated 6 weeks ago by
Aadil Rashid
•
0
•
written 23 months ago by
Hamid Ghaedi
2.7k
3
votes
0
replies
189
views
10
votes
5
replies
2.2k
views
6 follow
written 4.3 years ago by
mustafaazhar3
▴
60
23
votes
0
replies
2.1k
views
Tutorial:
Building Docker images
9 weeks ago by
ATpoint
65k
1
vote
1
reply
845
views
updated 9 weeks ago by
Vincent Laufer
★
2.4k
•
written 9 weeks ago by
kodwings
▴
10
83
votes
34
replies
14k
views
21 follow
76
votes
2
replies
51k
views
written 9.3 years ago by
Eric Normandeau
11k
14
votes
5
replies
10k
views
6 follow
Tutorial:
Easy way to do GO enrichment in R
updated 4 months ago by
Kevin Blighe
83k
•
written 4.8 years ago by
ahmad mousavi
▴
720
1
vote
0
replies
697
views
33
votes
7
replies
7.5k
views
9 follow
Tutorial:
Methylation Analysis Tutorial in R_part1
24 days ago by
Hamid Ghaedi
2.7k
3
votes
2
replies
765
views
Tutorial:
Running fastq_screen on your data
6 months ago by
rohitsatyam102
▴
640
7
votes
12
replies
1.3k
views
updated 7 months ago by
Shred
▴
870
•
written 7 months ago by
thehung92phuyen
▴
30
73
votes
14
replies
13k
views
15 follow
Tutorial:
List Of Bioinformatics Books
23
votes
13
replies
3.7k
views
9 follow
updated 8 months ago by
liorglic
▴
950
•
written 11 months ago by
Istvan Albert
94k
3
votes
13
replies
7.6k
views
12
votes
9
replies
2.6k
views
Tutorial:
TCGA transcriptome data to R (DESeq2)
updated 3 months ago by
dk0319
▴
30
•
written 9 months ago by
Barry Digby
★
1.0k
2
votes
0
replies
753
views
9 months ago by
sinha.shriprakash
▴
20
0
votes
0
replies
4.5k
views
12
votes
4
replies
3.9k
views
Tutorial:
*FREE course* Bioinformatics for Biologists: An Introduction to Linux, Bash Scripting, and R
updated 10 months ago by
iamsmor
•
0
•
written 19 months ago by
garden_giessen
▴
120
21
votes
10
replies
46k
views
9 follow
5
votes
2
replies
1.5k
views
12 days ago by
Hamid Ghaedi
2.7k
40
votes
6
replies
14k
views
Tutorial:
Greatly speed up conda by using mamba
updated 8 months ago by
cameron.cowan
▴
30
•
written 18 months ago by
rpolicastro
9.8k
141
votes
68
replies
40k
views
18 follow
updated 3 months ago by
Guido
•
0
•
written 4.8 years ago by
Kevin Blighe
83k
14
votes
1
reply
1.1k
views
193
votes
44
replies
66k
views
33 follow
updated 5 days ago by
Ram
37k
•
written 10.0 years ago by
Obi Griffith
20k
6
votes
2
replies
833
views
13 months ago by
Kevin Blighe
83k
0
votes
0
replies
738
views
2
votes
0
replies
1.1k
views
Tutorial:
Affymetrix HTA 2.0 id conversion
14 months ago by
Kevin Blighe
83k
45
votes
2
replies
34k
views
Tutorial:
Mapping Reads With Bwa And Bowtie
86
votes
99
replies
30k
views
24 follow
0
votes
0
replies
591
views
1
vote
0
replies
785
views
Tutorial:
Slurm and parallelization
1
vote
0
replies
707
views
12
votes
1
reply
1.5k
views
Tutorial:
PCR Primer or Primer+Probe design
updated 15 months ago by
jared.andrews07
★
13k
•
written 15 months ago by
Kevin Blighe
83k
114
votes
66
replies
37k
views
20 follow
4
votes
0
replies
715
views
Tutorial:
Long Read Genome Assembly Video Series
15 months ago by
pbpanigrahi
▴
420
0
votes
1
reply
585
views
Tutorial:
Add Customized Filters in GDC
updated 16 months ago by
cpad0112
21k
•
written 16 months ago by
Zhenyu Zhang
▴
580
61
votes
26
replies
9.1k
views
11 follow
12
votes
20
replies
10k
views
10 follow
16 months ago by
jared.andrews07
★
13k
4
votes
2
replies
1.8k
views
updated 16 months ago by
GenoMax
120k
•
written 3.3 years ago by
Shicheng Guo
★
9.2k
41
votes
13
replies
41k
views
9 follow
Tutorial:
Using R in Conda
updated 10 weeks ago by
Siddharth
•
0
•
written 2.2 years ago by
rohitsatyam102
▴
640
31
votes
9
replies
18k
views
11 follow
updated 4 months ago by
Verónica
•
0
•
written 2.1 years ago by
lavinia.gordon
▴
140
98
votes
16
replies
28k
views
18 follow
Tutorial:
Heatmaps in R
4 months ago by
Jean-Karim Heriche
26k
Recent Votes
Recent Locations •
All
United States, 1 minute ago
Hong Kong, 7 minutes ago
United States, 14 minutes ago
Peru, 14 minutes ago
Hong Kong, 16 minutes ago
China, 17 minutes ago
United States, 19 minutes ago
Recent Awards •
All
Popular Question to
Lee Katz
★
3.1k
Popular Question to
hkarakurt
▴
150
Popular Question to
bitpir
▴
210
Scholar to
jared.andrews07
★
13k
Great Question to
Kasthuri
▴
290
Popular Question to
saadleeshehreen
▴
100
Recent Replies
Comment: Check barcode collision
by
Vincent Laufer
★
2.4k
https://satijalab.org/seurat/reference/read10x
yes there is a specific function called read10x aimed at this sort of thing :-D
Answer: Tool for extracting part of aligned sequence by CIGAR string
by
cmdcolin
★
2.4k
this does not necessarily answer your question, but becoming familiar with parsing CIGAR is sometimes quite useful
Here is a short code th…
Comment: Error in converting vcf file to plink format
by
Madhawa
▴
10
Hi,
I have another issue when I work with this data set. After I obtain the BED, BIM and FAM files, I tried to do some QC steps for this d…
Answer: Create the design matrix for limma differential expression analysis.
by
Gordon Smyth
★
4.9k
See
[A guide to creating design matrices for gene expression experiments](https://bioconductor.org/packages/release/workflows/vignettes/RNA…
Answer: Should assemblies be removed if core gene alignment is identical?
by
Mensur Dlakic
★
20k
> Normally they should be excluded from the analysis.
It will not mess up statistics or anything like that, but there will be no separat…
Comment: for loop and sapply for assigning name
by
rpolicastro
9.8k
Untested since no example data was provided.
```
dfs <- lapply(list(df1, df2), \(x) {
colnames(x) <- info$name[which(info$id == colnames(…
Comment: Low alignment score for microRNA
by
ntsopoul
▴
10
Just for the record. I did the conversion with
sed '/^[^>]/s/U/T/g' mature.fa > mature_conv.fa
to avoid modification of the header an…
Comment: Understanding bowtie2 for short reference sequences
by
Sina
•
0
That was indeed my first approach, remove exact matches and then those with only substitutions (which are still relatively fast to identify…
Comment: Low alignment score for microRNA
by
GenoMax
120k
Since miRNA are small you will want to stick with an un-gapped aligner so `bowtie v.1.x` is a fine choice.
Comment: Low alignment score for microRNA
by
ntsopoul
▴
10
ok great I will try this. Maybe not in line with the thread but which aligner would you recommend to align the small-rna seq onto the genom…
Comment: Low alignment score for microRNA
by
GenoMax
120k
You could use `sed 's/U/T/g' mature.fa > conv.fa` as a quick brute force method. It may replace some `u` characters in fasta headers.
Answer: EDAseq, edgeR libraries cannot be installed in M2 mac
by
Gordon Smyth
★
4.9k
See https://stat.ethz.ch/pipermail/bioc-devel/2022-September/019178.html
PS. I'm curious why you don't sent such a Bioconductor-specific q…
Comment: EDAseq, edgeR libraries cannot be installed in M2 mac
by
GenoMax
120k
Can you install `samtools` via `conda`? That should include the `lzma.h` headers.
Comment: Low alignment score for microRNA
by
ntsopoul
▴
10
Oh thank you so much! This makes total sense…
So how dow I do the conversion and on which file? The mature.fa I guess …
Answer: Low alignment score for microRNA
by
GenoMax
120k
> Do I have to convert T to U?
Yes you have to do that conversion. Then align with a bowtie v.1.x index created after the conversion.
Traffic: 1475 users visited in the last hour
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by the
version 2.3.6
version 2.3.6