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12 results • Page
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Views
Votes
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0
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4
replies
251
views
Problem with fatsq-dump
fastq-dump
sratoolkit
4 hours ago by
Utpal
• 0
0
votes
1
reply
162
views
Remove part of headers in FASTA file
Fasta
updated 11 hours ago by
GenoMax
127k • written 1 day ago by
fatemeh
• 0
0
votes
2
replies
137
views
RNA Sequencing and Vg pan -transcriptome build
pantranscriptome
vg
ran-sequencing
pan
fast
genome
updated 6 hours ago by
Jordan M Eizenga
▴ 70 • written 17 hours ago by
kcarery
• 0
0
votes
1
reply
100
views
Log2 FC Threshold
GEO2R
updated 10 hours ago by
seidel
11k • written 13 hours ago by
leenkhoury282
• 0
0
votes
0
replies
97
views
CIBERSORTx Docker version
deconvolution
version
Docker
CIBERSORTx
19 hours ago by
Leite
★ 1.2k
0
votes
0
replies
94
views
Adding median value to VlnPlot in Seurat
Median
Seurat
17 hours ago by
Swati
• 0
0
votes
0
replies
89
views
What is the meaning of 'a too large, ITMAX too small in gamma countinued fraction (gcf)'
meta
analysis
GWAS
METAL
updated 11 hours ago by
GenoMax
127k • written 17 hours ago by
ymberzal
• 0
1
vote
0
replies
81
views
Minimap2 giving opposite strand orientation than Pychopper
nanopore
Pychopper
Minimap2
16 hours ago by
vanda.gaonach-lovejoy
▴ 10
0
votes
1
reply
70
views
how to import hdf5 Hi-C data into R using HiTC package
hdf5
importC
R
HiTC
updated 7 hours ago by
rpolicastro
11k • written 8 hours ago by
rheab1230
▴ 140
0
votes
0
replies
50
views
Emapplot Pie Graphic Legend Interferes with Map
enrichplot
clusterprofiler
Emapplot
8 hours ago by
raquel.ajalik
• 0
0
votes
0
replies
15
views
how to know what adapter sequences to trim for RNA-seq?
fastq
rnaseq
cutadapt
1 hour ago by
lunarskye222
• 0
0
votes
0
replies
10
views
module and trait correlation for WGCNA
treatment
WGCNA
relation
microarray
module-treatment
54 minutes ago by
Shriyansh
• 0
12 results • Page
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Recent Votes
downloading human gene symbol with duplicates
downloading human gene symbol with duplicates
Getting a list of protein coding genes in human
Answer: How to make cut off linein cluster,
How to make cut off linein cluster,
Answer: GetBM - GERP conservation score for GRCm39
Answer: Using STAR for RNA seq-alignment.
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Comment: Is it possible to do DGE analysis using log 2 normalized data with EdgeR ?
by
Adaline.D
• 0
That explains a lot to me. Thank you, seidel! They used Affymetrix Human Gene 1.0 ST Array chips. Hope you have a wonderful day.
Comment: How to make cut off linein cluster,
by
Info.shi
▴ 20
Thank you so much it worked. I highly appreciate your help.
Answer: How to make cut off linein cluster,
by
Jeremy
▴ 770
Try adding the following line of code: abline(h = .02)
Comment: Problem with fatsq-dump
by
Utpal
• 0
Thank you for your support. I tried the command conda install -c bioconda sra-tools But, still with the command, fastq-dump it return…
Comment: RNA Sequencing and Vg pan -transcriptome build
by
Jordan M Eizenga
▴ 70
The `vg mpmap` subcommand has features for mapping RNA-seq data to a graph. We describe in more detail in [this publication][1], including …
Comment: how to import hdf5 Hi-C data into R using HiTC package
by
rpolicastro
11k
From the error you may need to specify the file path instead of passing it the imported data.
Comment: RNA Sequencing and Vg pan -transcriptome build
by
cmdcolin
★ 2.9k
i am not sure how about the data input format but 'hisat2' is able to 'align rna-seq to a population reference'. this may be a little diffe…
Comment: Is it possible to do DGE analysis using log 2 normalized data with EdgeR ?
by
seidel
11k
What technology is the GEO data set derived from? Signal intensity implies a fluorescence read out (i.e. microarray). If that's the case, y…
Comment: Log2 FC Threshold
by
seidel
11k
Given that 0.2 is a 1.15 fold change (2^0.2) you're right to be skeptical, but there's no clear answer as to the significance. Consider tha…
Comment: Read lengths greater than insert length
by
GenoMax
127k
As I said above the adapters are each ~60 bp long so they add ~120 bp (5' and 3' end adapters) to the length of the DNA fragment. What you …
Comment: Problem with fatsq-dump
by
GenoMax
127k
Looks like the developers have an answer for this error: https://github.com/ncbi/sra-tools/issues/139 At least the program seems to be ins…
Comment: Read lengths greater than insert length
by
shpak.max
▴ 30
I'm not claiming that all fragment lengths are exactly 50, the typical range for my data is 45-60. However, my read lengths are all 150, so…
Answer: Read lengths greater than insert length
by
GenoMax
127k
Illumina libraries are made by adding adapters to the ends of DNA fragment(s). Those adapters themselves are about 60 nucleotides long. Not…
Answer: How to get fraction of unspliced reads for specific gene from scRNAseq Cell Rang
by
Rob
5.9k
If you have the raw data, you can easily get this information using [alevin-fry](https://www.nature.com/articles/s41592-022-01408-3). It pr…
Answer: Matching gene-expression data with clinical data: best practices.
by
pilargmarch
▴ 60
I really like using [the R/Bioconductor package TCGAbiolinks][1], it gives you clinical and expression data by patient ID. [1]: http…
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