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15 results • Page
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0
votes
5
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273
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Should I remove unlocalized scaffols in reference genome before alignment?
qualimap
alignment
minimap2
GRCh38
assembly
22 hours ago by
njornet
▴ 20
0
votes
4
replies
173
views
different FeatureCounts output for the same data
fpkm
Counts
Rsubread
rna-seq
1 hour ago by
sehriban.buyukkilic
▴ 10
1
vote
2
replies
149
views
alignment result
RNA-seq
samtools
hisat2
3 hours ago by
ahmad.sajad4541
• 0
0
votes
2
replies
208
views
How to calculate identity percentage between proteins contained in a FASTA file?
protein
FASTA
alignment
updated 14 hours ago by
Ram
43k • written 1 day ago by
v.berriosfarias
▴ 140
0
votes
1
reply
45
views
Highest variable features in single cell data
cell
single
updated 1 hour ago by
ATpoint
82k • written 2 hours ago by
Kazo
• 0
0
votes
1
reply
106
views
GEMMA GWAS how to specify factor or numerical for covariates
covariate
GEMMA
GWAS
updated 17 hours ago by
Sofia
• 0 • written 21 hours ago by
mawigoj318
• 0
0
votes
1
reply
117
views
Annovar using R package
Annovar
gnomAD
R
updated 10 hours ago by
Pierre Lindenbaum
161k • written 13 hours ago by
DKA
▴ 40
0
votes
0
replies
92
views
Sequence BLAST in plus/minus and plus/plus
blast
CRISPR
strand
sequencing
23 hours ago by
salias
• 0
0
votes
0
replies
12
views
Why not use iBAQ for calculating differential abundance of proteins?
protein
maxquant
18 minutes ago by
Aspire
▴ 300
0
votes
0
replies
139
views
roary not working with pgap output gff files with fasta sequence but works with prokka's gff outputs
pangenome
PGAP
NCBI
roary
Prokka
19 hours ago by
pramach1
▴ 40
0
votes
0
replies
86
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
TCGA
GDCprepare
updated 14 hours ago by
Ram
43k • written 19 hours ago by
glaciya2018
• 0
0
votes
0
replies
81
views
Alternative splicing analysis using SUPPA tool - how to normalise counts?
rna-seq
single-cell
suppa
alternative-splicing
updated 14 hours ago by
Ram
43k • written 1 day ago by
newuser2024
• 0
0
votes
0
replies
73
views
Is result interpretation of the modelHomotypic function of the DoubletFinder correct?
doublet
DoubletFinder
Seurat
modelHomotypic
updated 14 hours ago by
Ram
43k • written 1 day ago by
Jeyong
• 0
0
votes
0
replies
61
views
Can you give me an example of a small globular protein (PDB) that has disordered alpha-carbons?
protein
pdb
alpha-carbon
8 hours ago by
4fzcgueyp5
• 0
0
votes
0
replies
51
views
PCA plot
DESeq2
PCAplot
6 hours ago by
Aaliya
▴ 10
15 results • Page
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Recent Votes
Answer: Fetch table from clinvar database according to a list of rsid
Comment: Fetch table from clinvar database according to a list of rsid
Comment: Adding CB tag to bam file
Comment: alignment result
Comment: clustalo - align milions of short seq, memory issue
Answer: clustalo - align milions of short seq, memory issue
Comment: downloading genomes in fasta format from accession ids
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Answer: Finding orthologs between genome error
by
Adrian Altenhoff
★ 1.1k
Hi, thanks for letting us know. In a recent software update, we introduced a problem with the written splice information in the cached …
Comment: Fetch table from clinvar database according to a list of rsid
by
ashaneev07
▴ 20
so which one should i prefer? i don't need the entire results i need the condition-Germline table only. (for eg:-from, https://www.ncbi.nlm…
Comment: To get p-values for the TPM
by
dsull
★ 5.8k
OK, not sure why your intention is to use RSEM p-values for, but at least tell us the commands you ran then otherwise how are we supposed t…
Comment: Fetch table from clinvar database according to a list of rsid
by
Pierre Lindenbaum
161k
> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
Comment: different FeatureCounts output for the same data
by
sehriban.buyukkilic
▴ 10
Sure, I'll inquire about the version of Rsubread. I'll keep you posted if it works :) Thanks
Comment: different FeatureCounts output for the same data
by
sehriban.buyukkilic
▴ 10
Yeah, let me show you my featureCounts result, it looks like this. It's too low. [1]: /media/images/eb8293fe-e6ae-4b02-92e2-0ba2075b
Comment: Adding CB tag to bam file
by
Pierre Lindenbaum
161k
samtools addreplacerg is for read groups. This is not what OP asked.
Comment: Adding CB tag to bam file
by
Maria
• 0
When I try ``` samtools addreplacerg -r "@CB\tID:$cell" -o $cell.bam $LINE``` the CB tag gets add to the header, but the tag in every line …
Answer: Figures are disappeared from html report of SnpEff
by
Pierre Lindenbaum
161k
the remote website providing the javascript or/and the images is down or you're now behind a proxy. Check the firefox console: https://fire…
Comment: Fetch table from clinvar database according to a list of rsid
by
Pierre Lindenbaum
161k
ah ! and your code doesn't work because clinvar ID is not a rs-ID.
Answer: Fetch table from clinvar database according to a list of rsid
by
Pierre Lindenbaum
161k
$ cat input.rs rs11203366 rs11203367 rs874881 rs776453694 rs80324279 rs324420 rs112766203 wget -…
Comment: Highest variable features in single cell data
by
ATpoint
82k
> and these cells are not even in a single cluster. What does this mean? If you run clustering on all cells then every cell is assigned t…
Comment: Is it possible to get a list of representative genomes from a past RefSeq releas
by
Bertalan_Takacs
▴ 90
Yes, I can tell that, but as far as I see it doesn't contain any other information about the genomes, such as if they were representative i…
Answer: Hide positions in alignment with 99% "–" characters to ignore single sequence in
by
b.contreras.moreira
▴ 170
You can try <https://github.com/inab/trimal>
Comment: To get p-values for the TPM
by
VITALA
• 0
yes i want what rsem does and i did try with prior-enhanced option/pRSEM, but i think pRSEM is for chipseq data
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