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899 results • Page 3 of 18
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1
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5
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1.7k
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How to make bed file of TSS (approximately 2kb, 1 kb upstream and 1kb downstream) of genes
RNA-Seq
updated 13 days ago by 38k • written 2.7 years ago by • 0
1
vote
5
replies
692
views
Read count using htseq-count.
Assembly RNA-Seq gene
updated 13 days ago by 38k • written 2.0 years ago by • 0
2
votes
5
replies
559
views
msigdbr returns the same genesets for mouse as in for human,
msigdbr
updated 5 days ago by 13k • written 9 days ago by ▴ 30
3
votes
4
replies
1.5k
views
Which files from PacBio output files to use in downstream analysis in R
R PacBio
updated 4 days ago by 38k • written 18 months ago by ▴ 20
1
vote
4
replies
811
views
comparing every row in a file to find commom elements
Assembly genome sequence sequencing
updated 12 days ago by 38k • written 3.8 years ago by • 0
0
votes
4
replies
692
views
How to download the final reads of SRA data from NCBI using fastq-dumb
fastq fasta SRA
updated 9 days ago by 38k • written 21 months ago by ▴ 10
2
votes
4
replies
442
views
Trouble with transcripts_id when using how_are_we_stranded_here python package
bash sequencing RNA-seq
9 days ago by ashleymb1116 • 0
2
votes
4
replies
620
views
perseus expert assist
gene
updated 12 days ago by 38k • written 3.7 years ago by ▴ 10
0
votes
4
replies
1.4k
views
How to colour points in cnetplot of clustprofiler?
clusterprofiler cnetplot R
updated 2 days ago by • 0 • written 19 months ago by ▴ 20
0
votes
4
replies
1.1k
views
How to download FASTA file from psRNAtarget
FASTA sequence
updated 2 days ago by 38k • written 4.8 years ago by • 0
0
votes
4
replies
393
views
WGCNA hub genes VS. DEG
DE analysis WGCNA DEG
13 days ago by Kaia • 0
0
votes
4
replies
305
views
what does total count mean at a location in IGV
bam samtools igv
17 days ago by newDarkAB09834 ▴ 20
1
vote
4
replies
1.2k
views
biostars.org: Search capped to 50 hits?
meta biostars
updated 9 days ago by 38k • written 6.0 years ago by 14k
0
votes
4
replies
1.2k
views
Beginner problems: Aligning "genomes" that come in contigs
alignment whole-genome scaffold
updated 9 days ago by 38k • written 18 months ago by • 0
3
votes
4
replies
262
views
Creating sample groups from a combination of genes for survival analysis
Survival
4 days ago by krushnach80 ★ 1.1k
0
votes
4
replies
744
views
makedb process issue - Error: staxids output field requires setting the --taxonmap parameter #601
Diamond
updated 4 days ago by 38k • written 8 months ago by • 0
0
votes
4
replies
451
views
Large *.bam files difficult to open in UGENE
visualization UGENE BAM
updated 4 days ago by 38k • written 13 months ago by • 0
0
votes
4
replies
1.5k
views
Downloading unique data from refseq
fasta bacteria refseq
updated 9 days ago by 38k • written 6.9 years ago by • 0
3
votes
4
replies
1.4k
views
How to get regions with mapped reads
bed bam RNA-Seq bedtools
updated 4 days ago by 38k • written 4.5 years ago by ▴ 100
3
votes
4
replies
462
views
Genome Reference Consortium Human Build - Transcriptome Size Query
GRC
updated 9 days ago by 38k • written 10 months ago by • 0
3
votes
4
replies
330
views
How much reads per cell for fusion detection with Nanopore ?
single-cell fusion nanopore
3 days ago by Evan ▴ 180
1
vote
4
replies
193
views
Protein name in GenBank
genbank python biopython
updated 10 hours ago by 127k • written 16 hours ago by • 0
0
votes
4
replies
332
views
Between sample normalization without replicates
normalization RNA-Seq
13 days ago by GR ▴ 370
5
votes
4
replies
1.7k
views
MyVariant.info fields descriptions?
genome snp variant
updated 3 days ago by 38k • written 6.9 years ago by ▴ 90
1
vote
4
replies
351
views
Loading Traitdata file for WGCNA analysis
R WGCNA
updated 5 days ago by 38k • written 5 months ago by ▴ 50
1
vote
4
replies
1.1k
views
Agilent Sure Select .bed file v6 and v8
Agilent bed SureSelect
updated 4 days ago by 38k • written 18 months ago by • 0
3
votes
4
replies
482
views
Changing Temporary File Location for Local BLASTP to nr Database
protein blast nr
updated 6 days ago by 38k • written 10 weeks ago by ▴ 20
0
votes
4
replies
590
views
I want to merge gene sequences in fasta to create one genome from all cds region.
fasta linux genome
updated 6 days ago by 38k • written 10 weeks ago by • 0
0
votes
4
replies
575
views
CPTAC data download, transcriptomics
CPTAC transcriptome
updated 3 days ago by 38k • written 7 months ago by ▴ 160
18
votes
4
replies
8.1k
views
How To Find Rna-Seq Data Of Published Papers?
geo next-gen RNA-seq
updated 27 days ago by 38k • written 9.6 years ago by ▴ 930
0
votes
4
replies
1.7k
views
CIBERSORT: Errors were encountered in input files, run aborted:
deconvolution cibersort
updated 9 days ago by 38k • written 2.1 years ago by ★ 1.7k
0
votes
4
replies
448
views
Samtools sort results are different
samtools
updated 13 days ago by 38k • written 2.3 years ago by ▴ 20
0
votes
4
replies
334
views
WGCNA number of modules issue
networks gene WGCNA correlation
10 days ago by 1215045934 ▴ 80
2
votes
4
replies
240
views
Error with a function in ATAC-seq analysis
ATAC-seq
3 days ago by Chris ▴ 70
7
votes
4
replies
1.2k
views
So many Zeros (read counting)_NGS sequence analysis with R / Bioconductor: RNA-Seq workflow
alignment RNA-Seq R
updated 12 days ago by 38k • written 4.7 years ago by • 0
0
votes
4
replies
1000
views
Prokka "not a readable non-empty FASTA file"
fasta prokka
updated 9 days ago by 38k • written 11 months ago by • 0
0
votes
4
replies
1.0k
views
Help with whole genome alignment
alignment
updated 9 days ago by 38k • written 4.4 years ago by ▴ 60
0
votes
4
replies
1.3k
views
Is it possible for a cell cluster to not have cells of a certain condition?
seurat
updated 9 days ago by 38k • written 20 months ago by • 0
1
vote
4
replies
815
views
Repeat masking for genome annotation
masking annotation repeat
26 days ago by liorglic ★ 1.2k
7
votes
4
replies
1.7k
views
useful and freely available softwares for Bioinformatics
software
updated 9 days ago by 38k • written 8.0 years ago by ▴ 920
0
votes
4
replies
528
views
Filtlong and Flye
fastq
updated 4 days ago by 38k • written 5 months ago by • 0
0
votes
4
replies
605
views
Help needed
bioalcidae
updated 9 days ago by 38k • written 14 months ago by ▴ 50
2
votes
4
replies
586
views
Noob question: I want to use TCGA data to compare survival with mutations, how should I do it?
cancer mutations tcga
updated 9 days ago by 38k • written 10 months ago by ▴ 10
1
vote
4
replies
761
views
Method to classify given sample into subtype
Breast-Cancer RNA-Seq TCGA-BRCA TCGA
updated 9 days ago by 38k • written 2.5 years ago by • 0
0
votes
4
replies
911
views
Dealing with non overlapping reads
vsearch usearch sequencing illumina amplicon
updated 5 days ago by 38k • written 20 months ago by • 0
0
votes
4
replies
652
views
Single cell RNASeq data with only R2.fastq
RNA-Seq
updated 13 days ago by 38k • written 2.4 years ago by • 0
0
votes
4
replies
436
views
SPOT_ID
SPOT_ID
26 days ago by Kirstie Wong • 0
0
votes
4
replies
831
views
"Illegal instruction" error when I use the latest STARsolo to analysis 10X genomics data
statsolo 10x
updated 13 days ago by • 0 • written 20 months ago by ▴ 70
1
vote
4
replies
980
views
Oxford nanopore sequnces with unequal base content?
long-reads nanopore sequencing sequence
updated 17 days ago by 38k • written 2.6 years ago by • 0
0
votes
4
replies
936
views
Highly correlated modules with clinical trait does not cluster together in eigengene dendrogram, WGCNA.
microarray gene-expression WGCNA
updated 17 days ago by 38k • written 2.1 years ago by ▴ 10
899 results • Page 3 of 18
Recent Votes
Answer: GetBM - GERP conservation score for GRCm39
A: circos plot gene expression by RNA-Seq
Create Interval List for Picard CollectRNASeqmetrics
Answer: multiallelic variants
Answer: LIMMA calculates identical adj.P.Val for different proteins from proteomics
Comment: Hard clip fastq
Answer: Hard clip fastq
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Recent Replies
Comment: Installing rlang version 1.1.0 by Medha • 0
Password: bQFDPMHbbT I want to install ExomeDepth, these dependencies were not getting installed on its own so I installed it before insta…
Answer: getTable ignores query ranges by Kyle ▴ 10
The short answer is you can theoretically do this you just need to a) make your SNPs are two base-pairs in length (i.e. add 1 to the end) a…
Answer: Installing rlang version 1.1.0 by Lluís R. ★ 1.2k
Having a package duplicated means they are at a different `.libPaths()` sites. Check which version is in which directory and directly remov…
Answer: Somatic truth set by samuel ▴ 180
I think I have found an naswer to my own question. Should anyone have the same question as of March 2023 the relevant data and information…
Answer: GetBM - GERP conservation score for GRCm39 by Kyle ▴ 10
Final solution thanks to Ben's help:: # convert df to Grange. snp_gr <-makeGRangesFromDataFrame(BM_SNPs, seqnames.field = "seqnam…
Comment: GetBM - GERP conservation score for GRCm39 by Kyle ▴ 10
Perfect answer, thanks Ben!
Answer: MapSplice2 gives error if the thread count (-p value) is greater than 2 by vishal.koparde ▴ 10
Any updates??
Comment: how to know what adapter sequences to trim for RNA-seq? by lunarskye222 • 0
Do you happen to know if the middle part of this udi barcode (GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTCTACATATCTCG) is also part of the TruSeq a…
Comment: Hard clip fastq by GenoMax 127k
If you simply want the reads to be compatible in length then do not adapter trim.
Comment: Hard clip fastq by samuel ▴ 180
@ATpoint, so no adapter trimming first? Just trim the raw fastq?
Answer: Confused on strandedness, what are antisense transcripts? by dsull ★ 4.0k
Think of it on the DNA level: If the mRNA made is the same sequence as the "sense" DNA strand (except U's instead of T's), it is a "sense" …
Comment: Protein name in GenBank by GenoMax 127k
If you must do this programmatically then collect all cases where things differ in order of words (or number of words) like the example abo…
Answer: Hard clip fastq by GenoMax 127k
You can also use `reformat.sh` from [**BBMap suite**][1] as follows reformat.sh -Xmx2g in1=R1.fq.gz in2=R2.fq.gz out1=R1_trim.fq.gz …
Answer: Hard clip fastq by ATpoint 70k
Use `seqtk trimfq`. It makes sense to trim first to your desired length and then run identical downstream processing for a fair comparison.…
Comment: Protein name in GenBank by Mensur Dlakic ★ 23k
I think you either take time to do it properly, or you will end up missing some proteins. BLAST sequence search, even on 1500 genomes, can …
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