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745 results • Page
3 of 15
Sort: Votes
Rank
Views
Votes
Replies
5
votes
8
replies
2.7k
views
Difference between total number of reads in fastq file and no of bases/nt sequences in fastq file?
FASTQ
updated 5 days ago by
Ram
40k • written 23 months ago by
Fizzah
▴ 30
5
votes
3
replies
264
views
Batch effect consideration (re-seq the same sample twice)
RNA-seq
batch-effect
updated 6 days ago by
Ram
40k • written 6 days ago by
jkim
▴ 140
5
votes
4
replies
2.7k
views
Distance Tree For Gerp
conservation
phylogeny
updated 10 days ago by
Diana
• 0 • written 11.7 years ago by
Darked89
4.4k
5
votes
8
replies
2.0k
views
Distinguish between forward strand, plus strand, sense strand
pysam
strand
star
sam
updated 20 days ago by
Buwei
• 0 • written 14 months ago by
tien
▴ 10
5
votes
4
replies
517
views
6 follow
How to delete part of row names in a list in linux
Linux
updated 16 days ago by
Ram
40k • written 17 days ago by
Mousumi Akter
• 0
5
votes
2
replies
2.4k
views
CWL: Comments in Common Workflow Language
Common-Workflow-Language
cwl
updated 13 days ago by
Ram
40k • written 6.4 years ago by
kevin.o.oluoch
▴ 70
5
votes
7
replies
535
views
Can one sample t.test be used to determine statistical significance for log2FC values?
log2FC
T.test
updated 24 days ago by
dsull
★ 4.7k • written 26 days ago by
aUser
▴ 30
5
votes
8
replies
5.3k
views
6 follow
How to repair corrupted fastq files after sortmeRNA
software error
RNA-Seq
alignment
updated 7 days ago by
Tommaso
• 0 • written 5.6 years ago by
SMILE
▴ 170
5
votes
2
replies
351
views
How to calculate GC content of reads that mapped to a specific gene?
STAR
RNA-seq
19 days ago by
bioinfo
▴ 110
5
votes
12
replies
813
views
Converting custom VCF to standard VCF
VCF
10 days ago by
avelarbio46
▴ 30
4
votes
0
replies
153
views
Herald:
The Biostar Herald for Wednesday, September 06, 2023
herald
18 days ago by
Biostar
2.0k
4
votes
4
replies
2.9k
views
How to keep the top hits only in the output file of hmmscan?
hmmer
hmmscan
updated 3 days ago by
Ram
40k • written 3.1 years ago by
A_heath
▴ 140
4
votes
3
replies
504
views
interpreting results from pathway analysis
RNA-seq
kegg
clusterprofiler
GSEA
pathway-analysis
updated 17 days ago by
Ram
40k • written 10 weeks ago by
kng
▴ 30
4
votes
5
replies
434
views
Recapitulating a GenomeBrowser-style plot
IGV
genome-browser
29 days ago by
LChart
3.3k
4
votes
3
replies
383
views
Creating custom GTF file for use with Cellranger with barcode sequences
Cellranger
23 days ago by
stefano.iantorno
▴ 70
4
votes
12
replies
3.4k
views
6 follow
Sort gff3 on chromosome, position and then featuretype (gene, mRNA, exon, CDS)
gff3
updated 12 days ago by
alejandrogzi
▴ 30 • written 3.4 years ago by
William
★ 5.2k
4
votes
4
replies
386
views
DESeq2 analysis using two featureCounts generated from different studies
RNA-seq
DESeq2
2 days ago by
abedkurdi10
▴ 190
4
votes
1
reply
345
views
Herald:
The Biostar Herald for Monday, August 28, 2023
herald
updated 26 days ago by
Jesse
▴ 720 • written 27 days ago by
Biostar
2.0k
4
votes
5
replies
481
views
Pre-processing for single cell RNAseq: Hard thresholds, data (cluster)-driven or both?
scRNA-seq
7 days ago by
psm
▴ 100
4
votes
6
replies
2.6k
views
IDT vs primer 3 - PCR dimerisation
PCR
primer3
IDT
primer
updated 9 days ago by
Emrah
• 0 • written 3.1 years ago by
timothy.kirkwood
▴ 130
4
votes
4
replies
8.7k
views
MaxEntScan score interpretation
splice-scores
MaxEntScan
updated 14 days ago by
Akshita
• 0 • written 4.7 years ago by
ga87mit
▴ 20
4
votes
5
replies
351
views
SRA and Bioproject IDs
Bioproject
GEO
SRA
updated 27 days ago by
GenoMax
134k • written 27 days ago by
mrashad
▴ 70
4
votes
1
reply
1.9k
views
How to convert File to array of File? Type mismatch between source and sink, File to array
Common-Workflow-Language
cwl
updated 13 days ago by
Ram
40k • written 6.9 years ago by
karl.nordstrom
▴ 90
4
votes
0
replies
183
views
Herald:
The Biostar Herald for Wednesday, September 20, 2023
herald
4 days ago by
Biostar
2.0k
4
votes
7
replies
520
views
How is the format of the bed file for samtools ampliconclip
samtools
ampliconclip
updated 19 days ago by
aw7
▴ 210 • written 23 days ago by
ManuelDB
▴ 70
4
votes
3
replies
981
views
INSTALLING DEseq2 via conda
DEseq2
conda
RNA-seq
updated 5 days ago by
Ram
40k • written 4 months ago by
Fizzah
▴ 30
4
votes
2
replies
289
views
Normalisation on subset of genes
genechip
RNA-Seq
differential-expression
updated 19 days ago by
ATpoint
76k • written 19 days ago by
Mia
▴ 20
4
votes
2
replies
302
views
samtools ampliconclip option --strand is not working?
samtools
ampliconclip
16 days ago by
ManuelDB
▴ 70
4
votes
8
replies
702
views
SRA-toolkit installation: "fastq-dump not found"
fastq
SRA-toolkit
updated 16 days ago by
river
• 0 • written 12 weeks ago by
BioGuy
• 0
4
votes
7
replies
576
views
Help with Error: None of the requested features were found: PECAM1 in slot data
seurat
multiome
25 days ago by
Chris
▴ 180
4
votes
3
replies
258
views
blastn Command Not Found
abricate
linux
blastn
updated 12 days ago by
Ram
40k • written 12 days ago by
2Black_Cats
• 0
4
votes
8
replies
5.3k
views
Convert bed12 to GFF
bed
gff
bed12
updated 23 days ago by
Juke34
8.2k • written 6.6 years ago by
cmdcolin
★ 3.2k
4
votes
12
replies
834
views
bedops alternative for bedtools -unionbedg ?
bedtools
bam
coverage
bedops
bed
updated 9 days ago by
Alex Reynolds
35k • written 25 days ago by
Agastya
▴ 10
4
votes
3
replies
322
views
Fetch genomic region(s) from refseq genomes
ensembl
updated 28 days ago by
GenoMax
134k • written 28 days ago by
usr2
▴ 10
4
votes
5
replies
742
views
Getting Intron Positions from Amino Acid Sequences
acid
positions
amino
sequences
intron
16 days ago by
fafad046
• 0
4
votes
5
replies
573
views
Help with error scanpy
scanpy
11 days ago by
Chris
▴ 180
4
votes
2
replies
2.3k
views
Tutorial:
Building mosdepth on macOS
nim
mosdepth
updated 19 days ago by
GenoMax
134k • written 3.4 years ago by
ATpoint
76k
4
votes
9
replies
737
views
Which minimap2 parameters to set while performing mapping to avoid such mismatches
minimap2
22 days ago by
Mo
▴ 40
4
votes
2
replies
248
views
News:
Standalone NCBI ClusteredNR database now available for download
ClusteredNR
NCBI
standalone
BLAST
19 days ago by
PeterC_NCBI
▴ 330
4
votes
7
replies
721
views
How to subtract a number from protein IDs?
blast
updated 3 days ago by
Ram
40k • written 3.1 years ago by
A_heath
▴ 140
3
votes
2
replies
1.7k
views
Extracting Residuals from Differential Expression Model
statistics
residuals
limma
updated 18 days ago by
Gordon Smyth
★ 6.4k • written 4.2 years ago by
JourneyToAbyss
▴ 210
3
votes
2
replies
325
views
Differential gene expression analysis after transcriptome assembly with SPAdes
SPAdes
differential-expression
transcriptome-assembly
updated 23 days ago by
Istvan Albert
98k • written 23 days ago by
langziv
▴ 50
3
votes
1
reply
219
views
Finding the raw data used to build reference genomes
reference-genome
updated 17 days ago by
Ram
40k • written 17 days ago by
Aaron
• 0
3
votes
5
replies
386
views
Multiple sequence aligments - parallelisation
MSA
phylotranscriptomics
muscle
clustal
26 days ago by
Lada
▴ 30
3
votes
2
replies
1.7k
views
Problems drawing cytobands with karyoploteR
RNA-Seq
R
Bioconductor
updated 24 days ago by
bernatgel
★ 3.4k • written 4.5 years ago by
uxiavb
▴ 10
3
votes
2
replies
315
views
Identifying common DEGs among multiple datasets
R
DEG
updated 3 days ago by
Barry Digby
★ 1.2k • written 4 days ago by
Shma
• 0
3
votes
5
replies
388
views
Ensembl site unresponsive in clusterProfiler analyses
parallell
clusterProfiler
R
updated 17 days ago by
manaswwm
▴ 440 • written 19 days ago by
enanoide
• 0
3
votes
4
replies
349
views
Weighted analysis
RNA-seq
6 days ago by
Peter
• 0
3
votes
1
reply
1.2k
views
%% error in Rstudio
seurat
r
updated 2 days ago by
Ram
40k • written 2.1 years ago by
AbsaR
• 0
3
votes
7
replies
573
views
Nextflow - How to pass the yml format input file from an argument to channel as a list
python
groovy
yaml
nextflow
12 days ago by
kani
▴ 10
745 results • Page
3 of 15
Recent Votes
Comment: Hisat2 index and alignment question
Comment: Dotplot error: subscript out of bound
Comment: Dotplot : how to self-define the range of legend
Answer: Dotplot : how to self-define the range of legend
Convert SAM to BAM
A: Convert SAM to BAM
A: Bulk download of entire BioProject SRA
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★ 4.7k
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▴ 420
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Recent Replies
Comment: Assistance with Fungal Genome Annotation Using Maker and BLAST
by
Mensur Dlakic
★ 24k
It should be faster, though you are not telling us how many proteins are in your query file. I suggest you use as many threads as availabl…
Comment: Hisat2 index and alignment question
by
Athena
• 0
That worked! Thank you. Didn't know that was an option... now I know.
Comment: Assistance with Fungal Genome Annotation Using Maker and BLAST
by
Edoardo
• 0
I ran blastp with the following command: blastp \ -db /path/to/Annotation_db/uniprot_fungi.fasta \ -query MYGEN.maker.output/…
Comment: Hisat2 index and alignment question
by
Athena
• 0
Pathway of my reference genome ![reference index pathway][1] when I tried running this command `hisat2 -p 8 -x /path/to/musculus_index…
Comment: Dotplot : how to self-define the range of legend
by
Xuhao
• 0
Thanks for your kind help.
Comment: Dotplot : how to self-define the range of legend
by
zau saa
▴ 50
add `breaks = c(-1, -0.5, 0, 0.5, 1)` to `scale_colour_gradientn()`
Comment: Dotplot : how to self-define the range of legend
by
Xuhao
• 0
It works!!! Thanks so much. Can I ask one more question? How to change the "average expression" scale into "-1, -0.5, 0, 0.5, 1"?
Comment: Low Alignment rate
by
dsull
★ 4.7k
Did you run FASTQC to check the quality of your sequencing samples? Otherwise, try taking some the reads that failed to align, and run the…
Comment: Integrated Seurat object change name of the two conditions
by
Amitm
★ 2.2k
Hi, See this [prev. post][1] where I contributed to, on accessing the meta data slot in a seurat object. There is more than one way. [1…
Comment: scRNAseq Differential expression analysis
by
jared.andrews07
★ 15k
I appreciate this statement and it largely mirrors my own. Lior sometimes makes extremely salient and important points. Other times, he's t…
Comment: Highly inflated p-values in GWAS by regenie
by
cwwong13
▴ 20
Thanks @4galaxy77 . The first 10 PCs were included in the calculation of the trait residuals, but still results were highly inflated.
Comment: Hisat2 index and alignment question
by
Istvan Albert
98k
the most logical and simple explanation is that most likely the path to index is specified incorrectly show us the paths with say `ls` the…
Comment: How to change from gene_id to GeneID/EntrezID using R
by
Kevin Blighe
86k
It would have been good if you had mentioned the species in your opening question. Regarding the fact that it may not be related to Ensembl…
Comment: How to change from gene_id to GeneID/EntrezID using R
by
Nicolas
• 0
Thank you for your help but my data are not related to ENSMBL and im not working with any model organism that allow me to use the org packa…
Comment: How to change from gene_id to GeneID/EntrezID using R
by
Nicolas
• 0
The thing is that every tutorial i've seen here is about using biomrt but as i said my data are not related to ENSMBL and i dont have the c…
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