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352 results • Page
4 of 8
Sort: replies
Rank
Views
Votes
Replies
1
vote
1
reply
236
views
--busco_db and --busco_seed_species with RNA-seq
RNA-seq
Funannotate
busco
14 days ago by
sansan_96
▴ 50
1
vote
1
reply
161
views
Testing the effect of the salinity water on abundance estimates
Salinity
updated 23 days ago by
ATpoint
81k • written 23 days ago by
Thibaut
▴ 10
0
votes
1
reply
198
views
Extract Umi sequence to readname
Sequence
FgBio
UMI
updated 7 days ago by
GenoMax
140k • written 7 days ago by
Smilesky
• 0
0
votes
1
reply
222
views
deepTools computeMatrix output import into R for enrichment calculations
R
deeptools
computeMatrix
deepTools
updated 13 days ago by
Pierre Lindenbaum
160k • written 13 days ago by
eeb74
• 0
0
votes
1
reply
146
views
NCBI gene data
Variants
NCBI
updated 3 days ago by
GenoMax
140k • written 3 days ago by
chandrakala.m
• 0
2
votes
1
reply
143
views
Computing the neighborhood graph in single cell pipeline
single-cell
knn
updated 17 days ago by
ATpoint
81k • written 17 days ago by
QX
• 0
1
vote
1
reply
279
views
Advice for genetic diversity stats analysis with both variant and variant sites
pi
diversity
vcf
genetics
updated 7 days ago by
dthorbur
★ 1.7k • written 8 days ago by
ekirsch
• 0
0
votes
1
reply
132
views
SNP VCF files from hybrid populations and parental populations generated by GBS in public databases
contaminations
verification
parental
check
updated 1 day ago by
Ram
43k • written 1 day ago by
Hajar
• 0
0
votes
1
reply
254
views
I can't add VAF from population for all of my variants from VCF file
vaf
vcf
genomics
gnomad
allelicfrequency
updated 12 days ago by
Arton
• 0 • written 14 days ago by
Samuel
▴ 20
0
votes
1
reply
123
views
How can I remove duplicate SNP?
plink
updated 1 day ago by
iraun
6.2k • written 1 day ago by
Zhennan
• 0
1
vote
1
reply
154
views
Pool-Seq same as normal variant calling?
Pool-Seq
Variant-Calling
updated 2 days ago by
dthorbur
★ 1.7k • written 2 days ago by
andrebolerbarros
• 0
1
vote
1
reply
182
views
How to determine if a somatic mutation alters transcription factor binding site?
cancer
motif
TFBS
somatic-mutation
updated 23 days ago by
Ram
43k • written 23 days ago by
ConvolutedGenome
▴ 20
0
votes
1
reply
203
views
Getting error in alignment using STAR
STAR
Error
updated 5 days ago by
Michael
54k • written 5 days ago by
pavithra.bioinformatics
• 0
0
votes
1
reply
168
views
seaborn dispersion graph
graph
dispersion
seaborn
updated 23 days ago by
Shred
★ 1.4k • written 23 days ago by
brunofelicianodeomena
• 0
0
votes
1
reply
225
views
Where to find a GTF, GFF, or SAF for RheMac2 genome
Annotations
updated 27 days ago by
GenoMax
140k • written 27 days ago by
Sillyman
• 0
1
vote
1
reply
175
views
Troubleshooting a REGENIE sex-stratified GWAS
GWAS
REGENIE
updated 9 days ago by
Corentin
▴ 600 • written 10 days ago by
s.may-wilson
▴ 50
0
votes
1
reply
176
views
Resources regarding Proteomics (In-Silico)
proteomics
docking
protein
molecular-simulation
updated 9 days ago by
Ram
43k • written 9 days ago by
Saurabh
• 0
0
votes
1
reply
156
views
Difference in relative abundance between MicrobiomeDB and r phyloseq
phyloseq
updated 4 days ago by
Chris Dean
▴ 390 • written 4 days ago by
benkosta
• 0
0
votes
1
reply
73
views
vcf file: number of samples does not match number of columns
vcf
bcftools
updated 7 hours ago by
Pierre Lindenbaum
160k • written 7 hours ago by
ekirsch
• 0
1
vote
1
reply
214
views
How to download raw data such as fastq file from MG-RAST?
MG-RAST
updated 25 days ago by
GenoMax
140k • written 25 days ago by
Adi
▴ 10
0
votes
1
reply
672
views
SQK-LSK112 adapter sequences
Nanopore
updated 28 days ago by
Nicolas Lichilin
▴ 20 • written 19 months ago by
zack.saud
▴ 50
0
votes
1
reply
124
views
DMRcate for sequencing data
DMRcate
DNA-methylation
differential-methylation
updated 8 days ago by
Basti
★ 1.9k • written 17 days ago by
alejandrarodrigu21
• 0
0
votes
1
reply
191
views
Running Pangolin
Pangolin
Splicing
updated 20 days ago by
Ram
43k • written 20 days ago by
Sruthi
• 0
0
votes
1
reply
158
views
Issues With Cram -> Fastq from GTEx v8 WGS
fastq
GTEx
cram
updated 9 days ago by
Pierre Lindenbaum
160k • written 9 days ago by
Vullnet
• 0
1
vote
1
reply
216
views
Integrate Chipseq and Atacseq data?
ATAC-seq
Chip-Seq
updated 27 days ago by
Yogi
▴ 70 • written 28 days ago by
DINESHR
▴ 10
0
votes
1
reply
127
views
Bed file
bedfile
updated 14 days ago by
Pierre Lindenbaum
160k • written 14 days ago by
Jeet
• 0
0
votes
1
reply
226
views
Issue with bigWigSummary utility of Kent/UCSC utilities
bigWig
UCSC
updated 13 days ago by
Pierre Lindenbaum
160k • written 13 days ago by
eeb74
• 0
0
votes
1
reply
224
views
Resolution of ambiguous calls in germline vcf
vcfs
germline
qc
updated 27 days ago by
Jeremy Leipzig
22k • written 28 days ago by
Raygozak
★ 1.4k
0
votes
1
reply
236
views
updateR() error
R
update
updated 10 days ago by
dthorbur
★ 1.7k • written 13 days ago by
marco.barr
▴ 30
2
votes
1
reply
219
views
ATAC-seq downstream analysis
ATAC-seq
diffbind
updated 29 days ago by
ATpoint
81k • written 4 weeks ago by
maplewj
▴ 10
0
votes
1
reply
186
views
Computing mid parent value for DE analysis
EdgeR
limma
DESeq2
updated 20 days ago by
Gordon Smyth
★ 6.9k • written 8 weeks ago by
pl23
• 0
0
votes
1
reply
149
views
Autodock tools error - The requested operation requires lifting
Autodock
MGLTools
updated 2 days ago by
zx8754
11k • written 3 days ago by
DOMENICA ALEXANDRA
• 0
0
votes
1
reply
750
views
Error in genetics vcf file - !! Error (genfile::MalformedInputError): Source "file-path/data_chrxx.vcf.gz" is malformed on line 5145934..
vcf
genetics
updated 3 days ago by
m.medinagomez
• 0 • written 2.3 years ago by
Nance
• 0
0
votes
1
reply
635
views
Multiple replicates with one SoapDenovo-Trans run?
rna-seq
soapdenovo-trans
transcriptome
updated 29 days ago by
nargisbashir10
• 0 • written 2.3 years ago by
nina.maryn
▴ 30
0
votes
1
reply
173
views
Troubleshooting poor DP values
Illumina
GATK
updated 22 days ago by
Pierre Lindenbaum
160k • written 22 days ago by
manfi
▴ 10
1
vote
1
reply
247
views
BAM to CRAM and BAM recover with smaller size
BAM
samtools
CRAM
updated 13 days ago by
GenoMax
140k • written 13 days ago by
geocarvalho
▴ 360
0
votes
1
reply
106
views
Wanting to make a Venn diagram of ATACseq peak files, unsure of where to start
ATAC-seq
updated 1 day ago by
Yogi
▴ 70 • written 1 day ago by
Ronin
• 0
0
votes
1
reply
151
views
How to perform enrichment p-value for a motif
Enrichment
statistics
updated 17 days ago by
Trivas
★ 1.7k • written 17 days ago by
Apex92
▴ 280
0
votes
1
reply
186
views
PEAR seems to have sense to me
PEAR
updated 8 days ago by
GenoMax
140k • written 8 days ago by
ManuelDB
▴ 80
0
votes
1
reply
83
views
Number of CPUs to use by DRAP for transcriptomic assmbly
DRAP
CPU
transcriptomics
updated 12 hours ago by
GenoMax
140k • written 14 hours ago by
Mohamed Abderrahmane
▴ 10
0
votes
1
reply
149
views
Download all phytochemicals from IMPPAT database
Phytochemicals
docking
IMPPAT
17 days ago by
goyalsamta2609
• 0
0
votes
1
reply
142
views
Cell communacations analysis. I only have the proteome of one type of cell
How
to
updated 1 day ago by
ATpoint
81k • written 2 days ago by
David Arturo
• 0
0
votes
1
reply
89
views
(sc)RNA-seq dataset for these cell lines: HEK293, HeLa, PC3 and U2OS
scRNA-seq
updated 15 hours ago by
Ram
43k • written 15 hours ago by
chiditatawmbi
• 0
0
votes
1
reply
200
views
Pathway activity in Bulk-RNA-SEQ analysis
R
RNA-seq
transcriptomics
updated 14 days ago by
jared.andrews07
★ 16k • written 14 days ago by
PBC
▴ 10
0
votes
1
reply
227
views
PCA script correction
correction
script
PCA
updated 6 days ago by
BioinfGuru
★ 1.6k • written 6 days ago by
prity6459
• 0
0
votes
1
reply
159
views
Mutation, MAF, CPTAC-3
CPTAC
mutation
updated 23 days ago by
marco.barr
▴ 30 • written 23 days ago by
Rob
▴ 170
0
votes
1
reply
208
views
Visualize and access gvcf/vcf files
genomics
vcf
updated 21 days ago by
vinayjrao
▴ 250 • written 4 weeks ago by
QX
• 0
0
votes
1
reply
159
views
Adding gene to GRange objects with single base
GRanges
genomics
updated 7 days ago by
ATpoint
81k • written 8 days ago by
QX
• 0
0
votes
1
reply
204
views
Calculating Species Abundance/Richness in Excel
species-abundance
Excel
updated 22 days ago by
Ram
43k • written 23 days ago by
ilsa
• 0
0
votes
1
reply
172
views
BRIG coverage.graph issues
BRIG
sam
updated 11 days ago by
Pierre Lindenbaum
160k • written 11 days ago by
dlera.lozano
• 0
352 results • Page
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Answer: log2(TPM+1)
Comment: Error in openning FastQC
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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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