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34 results • Page
1 of 1
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
7
views
Mapping ortholog human and mouse transcript
biomart
36 minutes ago by
1769mkc
★ 1.2k
0
votes
0
replies
12
views
Bowtie2 alignment rate
galaxy
alignment
Bowtie
rate
1 hour ago by
pavithraashokkumar818
• 0
0
votes
0
replies
14
views
Variant calling of GBS data for polyploid plant
GBS
variants
polyploid
plant
2 hours ago by
analyst
▴ 10
0
votes
0
replies
22
views
Convert to ENTREZGENE
maize
ENTREZGENE
5 hours ago by
sansan_96
▴ 50
1
vote
0
replies
29
views
Synthetic lethality and cancer database
interaction
lethal
synthetic
6 hours ago by
Shicheng Guo
★ 9.4k
0
votes
0
replies
33
views
Tissue specific mRNA expression dataset in human and mouse
tissue
specificity
8 hours ago by
Shicheng Guo
★ 9.4k
0
votes
1
reply
82
views
vcf file: number of samples does not match number of columns
vcf
bcftools
updated 9 hours ago by
Pierre Lindenbaum
160k • written 10 hours ago by
ekirsch
• 0
0
votes
4
replies
185
views
Is it reasonable to discard reads that show variation of quality across its length?
Trimming
8 hours ago by
BRENO
• 0
0
votes
2
replies
111
views
Error running local blastn in R using system2
blastn
NCBI
R
updated 8 hours ago by
Mensur Dlakic
★ 26k • written 11 hours ago by
Harrison
• 0
0
votes
1
reply
69
views
Looking for RPIP Illumina kit probe sequences
Sequences
Illumina
updated 14 hours ago by
GenoMax
140k • written 14 hours ago by
David Tachiquín
• 0
0
votes
9
replies
276
views
Low number of both surviving reads after trimming
trimmomatic
trimming
9 hours ago by
Jay
• 0
0
votes
1
reply
86
views
Number of CPUs to use by DRAP for transcriptomic assmbly
DRAP
CPU
transcriptomics
updated 14 hours ago by
GenoMax
140k • written 16 hours ago by
Mohamed Abderrahmane
▴ 10
3
votes
2
replies
98
views
Gene reads all zero for each sample
R
salmon
DE
DESeq2
15 hours ago by
DYLAN NICO
• 0
0
votes
0
replies
62
views
Contradictions in GSEA results
GSEA
Enrichment-analysis
PEA
updated 16 hours ago by
Ram
43k • written 16 hours ago by
Tolga
▴ 20
0
votes
0
replies
57
views
Illumina Dna Prep kit for sequencing phage linear genomes
tagmentation
transposons
phagetermini
sequencing
16 hours ago by
alenew.am
• 0
0
votes
3
replies
333
views
FindAllMarkers not working (Error (data layers are not joined. Please run JoinLayersWarning: When testing 1 versus all)
FindAllMarkers
seurat
re-clustering
16 hours ago by
Nitin
• 0
0
votes
1
reply
92
views
(sc)RNA-seq dataset for these cell lines: HEK293, HeLa, PC3 and U2OS
scRNA-seq
updated 17 hours ago by
Ram
43k • written 17 hours ago by
chiditatawmbi
• 0
0
votes
1
reply
115
views
Normalization strategies for comparing mapped reads across samples in RNA-seq
normalization
rnaseq
updated 16 hours ago by
Ram
43k • written 18 hours ago by
Picasa
▴ 640
0
votes
0
replies
76
views
How to change alternate conformation occupancy ?
Bio.PDB.Atom
Bio.PDB
biopython
updated 16 hours ago by
Ram
43k • written 19 hours ago by
udakshi
• 0
0
votes
0
replies
93
views
Training
chip-seq
ScATAC-seq
19 hours ago by
Manhezz
• 0
1
vote
2
replies
124
views
Flow Cytometry Data Analysis by Seurat
Seurat
updated 15 hours ago by
Ram
43k • written 20 hours ago by
gdfsnkfns
• 0
1
vote
11
replies
306
views
struggle to get fasta files from ucsc goldenPath
ucsc
getfasta
fasta
updated 14 hours ago by
GenoMax
140k • written 20 hours ago by
Lila M
★ 1.2k
2
votes
2
replies
122
views
Volcano Plot Output Inquiry: Graphs Facing Down
rstudio
volcano-plot
updated 15 hours ago by
dariober
14k • written 21 hours ago by
Pumla
• 0
0
votes
1
reply
94
views
Merging featureCounts output for different species
featureCounts
RNA-seq
updated 13 hours ago by
Ram
43k • written 21 hours ago by
Christian
• 0
0
votes
0
replies
74
views
Combine rename and rmdup in SeqKit to remove duplicate sequences and append N in header? Sort by occurence?
seqkit
fasta
21 hours ago by
Broccoli
• 0
0
votes
0
replies
70
views
Is there a good tool/reference for PBP and porin analysis
PBP
porin
22 hours ago by
blur
▴ 280
0
votes
0
replies
83
views
meta-analysis on RNA seq AND microarray results
microarray
RNA
22 hours ago by
liuyibin2005
• 0
0
votes
0
replies
67
views
SPOTlight deconvolution logFC, logFC cohen or mean.AUC
spatial-transcriptomics
SPOTlight
logFC
deconvolution
updated 17 hours ago by
Ram
43k • written 23 hours ago by
M'zelle
• 0
2
votes
10
replies
726
views
Only one read per run - Trying to use CellRangerv7
Fastq
CellRanger
updated 17 hours ago by
Ram
43k • written 5 weeks ago by
Sky
▴ 10
0
votes
8
replies
419
views
STAR aligner options
STAR
21 hours ago by
theophile
• 0
0
votes
4
replies
244
views
Coverage observed in introns in the Knockdown genes but not in knockout genes
RNA-seq
STAR
IGV
20 hours ago by
rohitsatyam102
▴ 840
1
vote
12
replies
544
views
Nanopore data filtering using fastp
fastp
nanopore
16 hours ago by
emilydolivo97
• 0
0
votes
5
replies
317
views
Parsing fasta file by coordinates
linux
fasta
updated 14 hours ago by
GenoMax
140k • written 3 days ago by
sorrymouse
▴ 120
0
votes
9
replies
461
views
Nextflow ERROR : Timeout waiting for connection from pool
nextflow
updated 19 hours ago by
GenoMax
140k • written 6 days ago by
dzisis1986
▴ 70
34 results • Page
1 of 1
Recent Votes
Comment: Gene reads all zero for each sample
Synthetic lethality and cancer database
Answer: log2(TPM+1)
Comment: Error in openning FastQC
Comment: F*up Night style events for Bioinformatics ? Comment if you're interested!
Answer: F*up Night style events for Bioinformatics ? Comment if you're interested!
Answer: F*up Night style events for Bioinformatics ? Comment if you're interested!
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Recent Awards •
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Teacher
to
Pierre Lindenbaum
160k
Popular Question
to
brian.fristensky
▴ 460
Popular Question
to
Ann
★ 2.4k
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GenoMax
140k
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Devon Ryan
104k
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amitpande74
▴ 20
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beacamara
• 0
Recent Replies
Answer: Is RNAseq data from a monoclonal cell line technically considered scRNAseq?
by
Soheil
▴ 90
Bulk RNAseq from any sample is still considered a bulk sample. Running bulk RNA sequencing on a sample with any level of cell type/state c…
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
BRENO
• 0
Yikes. Well, this is from an Illumina MiniSeq. Sure, I will use alignment, but only to remove host reads. Then the remaining reads will go …
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
GenoMax
140k
This is going to be tough to diagnose. Are you going to align to a reference? If so go ahead with the alignments to see if alignments turn …
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
BRENO
• 0
Thank you for replying. I have separated the reads with at least one N on them and they account for 0.2% of the total reads in the file (8'…
Comment: Error running local blastn in R using system2
by
Mensur Dlakic
★ 26k
The `-db data/nt_euk` switch means that in your current directory you have a subdirectory called `data`, and all the `nt_euk` files are in …
Comment: Low number of both surviving reads after trimming
by
Jay
• 0
Thank you for your opinion. I will try with lower LEADING and TRAILING bases. By the way, I tried to set `keepBothReads:true` through sear…
Comment: Error in openning FastQC
by
GenoMax
140k
At this point it would be beneficial to learn some of the basics of command line. Please use this UNIX tutorial since you seem to be new to…
Comment: vcf file: number of samples does not match number of columns
by
Pierre Lindenbaum
160k
> ore or have any suggestions for fixing it? it's a problem with your upstream process. You'd better fix it.
Comment: Error in openning FastQC
by
friszd
• 0
after running fastqc -o output.html input.fastq, terminal returns: " Specified output directory 'output.html' does not exist " , when i run…
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
GenoMax
140k
The question you should be looking into is why the Q scores are dropping there? Are there `N` calls indicating some issue with that cycle?
Comment: Error in openning FastQC
by
GenoMax
140k
What is `ctrl+c ctrl+v`? You may actually be killing the running fastqc process. If you run `fastqc` interactively (like what was shown ab…
Comment: F*up Night style events for Bioinformatics ? Comment if you're interested!
by
Dave Carlson
★ 1.7k
Ugh. I've definitely done this one before as well. And was none too happy about it.
Comment: Error in openning FastQC
by
friszd
• 0
fastqc -o output.html input.fastq ctrl+c ctrl+v
Comment: Error running local blastn in R using system2
by
GenoMax
140k
What do you see if you `cat nt_euk.nal`? Do the number of pieces mentioned in that file match with what you locally have?
Comment: Low number of both surviving reads after trimming
by
GenoMax
140k
It is your data and if you want to do that it is up to you. You may be throwing away essentially good data (you should remove the nextera s…
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