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15 results • Page
1 of 1
Sort: replies
Rank
Views
Votes
Replies
3
votes
4
replies
179
views
Invalid CIGAR after using bam clipOverlap
validatesamfile
cigar
bam
clipoverlap
8 hours ago by
MboiTui
▴ 20
1
vote
2
replies
258
views
Failed to download data from EBI with ascp
EBI
aspera
updated 9 hours ago by
孝中
• 0 • written 6 weeks ago by
biock
▴ 60
1
vote
2
replies
207
views
Setting a threshold on gene expression for subsetting (scRNA-seq)
scRNA-seq
updated 23 hours ago by
LauferVA
4.2k • written 2 days ago by
carolofharvest
▴ 40
0
votes
2
replies
204
views
perl Error - needLargeMem Bigwig
Bigwig
perl
mitosalt
5 hours ago by
marco.barr
▴ 130
0
votes
1
reply
41
views
Salmon vs Kallisto vs RSEM
quantification
kallisto
Salmon
transcriptomic
RSEM
updated 14 minutes ago by
Rob
6.6k • written 2 hours ago by
Mohamed Abderrahmane
▴ 20
0
votes
1
reply
154
views
How to decrease the motif score?
scores
Motif
updated 8 hours ago by
ATpoint
82k • written 2 days ago by
Hadia
• 0
0
votes
1
reply
175
views
BAM to Bedgraph creating an empty file
Bisulfite-seq
bismark
updated 4 hours ago by
raphael.B
▴ 520 • written 3 days ago by
irebekah.c
• 0
0
votes
0
replies
42
views
Help me with simple data for RNA seq
seq
RNA
DESeq2
R
1 hour ago by
vmpsb
• 0
1
vote
0
replies
58
views
Search within posts based on tags using the Biostars API
api
meta
biostars
6 hours ago by
Bálint
▴ 10
0
votes
0
replies
55
views
Subset of Transcripts- How do I proceed with it?
Stringite
Quantification
6 hours ago by
Varsha
• 0
0
votes
0
replies
55
views
Imputed data doesn't match directly genotyped APOE genotype
APOE
directgenotyping
imputation
16 hours ago by
kl
▴ 10
0
votes
0
replies
73
views
Tubemap multiseq
vg
23 hours ago by
karciharun42
• 0
0
votes
0
replies
61
views
virus genome annotation
annotation
gff3
consensus
NCBI
coding_regions
2 hours ago by
Ghada
• 0
0
votes
0
replies
44
views
PyRMD
Virtual
Screening
learning
cheminformatics
machine
8 hours ago by
s
• 0
0
votes
0
replies
60
views
Determining rs ids from SNP HGV base ID?
base
RsID
SNP
ID
HGV
15 hours ago by
Katherine
• 0
15 results • Page
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Answer: How do i calculate the mean of triplicates in a data.frame based on pattern?
How do i calculate the mean of triplicates in a data.frame based on pattern?
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C: The Biostar Handbook. A bioinformatics e-book for beginners.
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Recent Replies
Comment: Salmon vs Kallisto vs RSEM
by
Rob
6.6k
It's nice that you've gone ahead and done some analysis of these results and their differences on your data yourself. These more general qu…
Comment: Python script to query GeneCards to get EntrezID, symbol from Ensembl geneID
by
Mike Smith
★ 2.0k
In this location there is an "entrez" file which maps ensembl IDs to Entrez. It's probably as definitive as you're going to find: https://…
Comment: Python script to query GeneCards to get EntrezID, symbol from Ensembl geneID
by
Anya
• 0
Tried it just recently with almost the same results. 456 out of 496 IDs for protein-coding genes returned as "NA" even though I can see NCB…
Answer: Download All The Bacterial Genomes From Ncbi
by
2284046470
• 0
wget https://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/assembly_summary.txt awk -F '\t' '{if($12=="Complete Genome" && $11=="latest") p…
Answer: How do i calculate the mean of triplicates in a data.frame based on pattern?
by
dariober
14k
I'm a happy user of [data.table](https://rdatatable.gitlab.io/data.table/): ``` library(data.table) dat <- structure(list(sgrna = c("Cont…
Comment: How do i calculate the mean of triplicates in a data.frame based on pattern?
by
Assa Yeroslaviz
★ 1.9k
I know it can be done with something like that: ``` cbind(p767.AM = (rowMeans(p767[,2:4])), p767.MM = (rowMeans(p767[,5:7]…
Comment: How to add Ensembl ids after Pseudobulk analysis by DESeq2
by
ATpoint
82k
Why is your `GeneName` column in mapped a mix of Ensembl IDs and gene names? What Jared wants to say is that during the preprocessing you s…
Comment: Python script to query GeneCards to get EntrezID, symbol from Ensembl geneID
by
GenoMax
142k
> only give me partial results It is possible that not every Ensembl ID is going to convert to Entrez ID. Have you tried: https://www.b…
Comment: BAM to Bedgraph creating an empty file
by
raphael.B
▴ 520
You have a space in your reference path. Not sure it's intended?
Comment: Python script to query GeneCards to get EntrezID, symbol from Ensembl geneID
by
Anya
• 0
Do you have any recommendations of such sources or how to search for them? I'm a newbie and I need to convert GRCh38 Ensembl IDs to Entrez …
Comment: Python script to query GeneCards to get EntrezID, symbol from Ensembl geneID
by
Shred
★ 1.4k
Genecards added a footer saying that >SCRAPING AND OTHER AUTOMATED DOWNLOAD AND USE OF GENECARDS DATA STRICTLY PROHIBITED While this is …
Comment: perl Error - needLargeMem Bigwig
by
marco.barr
▴ 130
I managed to correct and solve the problem. It was due to issues with memory parameter settings on different login nodes. Additionally, I h…
Answer: Python script to query GeneCards to get EntrezID, symbol from Ensembl geneID
by
Anya
• 0
Here's a slightly changed version of this script. I changed line 42 from `'title':'NCBI Entrez Gene'` to `'title':'NCBI Gene'` ). And…
Comment: How do we do quantification using stringtie merge option for all the merged samp
by
Varsha
• 0
Thank you for the detailed explanation.
Answer: How can run cd-hit-est with a clstr threshold less than 0.8?
by
Asaf
10k
For future reference The 0.8 identity threshold for EST (nucleotides) is hardcoded. However, there's an option to use `-D` (distance) in…
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