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121,906 results • Page 677 of 2439
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7
votes
14
replies
4.1k
views
Repeat masking problem
repeatmasking ngs repeatmasker
4.4 years ago by Shri hari ▴ 40
0
votes
0
replies
711
views
Resistome Analyzer Report
bwa metagenomic resistome
4.5 years ago by Bio_Crap • 0
1
vote
1
reply
1.2k
views
KEGG Data retrieval
enzymeID KEGG
updated 2.5 years ago by 45k • written 4.5 years ago by • 0
0
votes
4
replies
1.7k
views
extract unmapped reads from WGS data - which samtools parameters to choose
WGS Sequencing
updated 4.5 years ago by ▴ 590 • written 4.5 years ago by ▴ 140
1
vote
1
reply
875
views
Identifying gene sequence in RNA-Seq data
sequence genomic rna-seq alignment
4.5 years ago by snow4964 ▴ 10
0
votes
3
replies
1.7k
views
WGCNA Timepoint Analysis
WGCNA rna-seq celltypes
updated 4.5 years ago by 89k • written 4.5 years ago by • 0
0
votes
4
replies
1.6k
views
SnpEff not correctly annotating multiple-nucleotide polymorphisms
annotation snpEff
4.5 years ago by Thoth • 0
3
votes
5
replies
3.1k
views
Fast parsing genbank files
Genbank parsing R
updated 4.4 years ago by 103k • written 4.5 years ago by ▴ 270
0
votes
2
replies
2.1k
views
Gene Labels (ggplot2)
labels ggplot2 R
updated 4.5 years ago by 9.8k • written 4.5 years ago by ▴ 100
0
votes
9
replies
5.7k
views
When converting .ped, .bim and .fam files to .pgen, .psam and .pvar in PLINK2
.pvar Plink2
updated 4.5 years ago by 11k • written 4.5 years ago by • 0
3
votes
1
reply
960
views
HI-C analysis in the cloud environment
HI-C
updated 4.5 years ago by ▴ 380 • written 4.6 years ago by ★ 1.4k
1
vote
5
replies
2.9k
views
Efficient way to perform fastq filtering of contaminants by read name prior to transcriptome assembly?
trinity BBmap transcriptome filtering assembly
updated 4.5 years ago by 153k • written 4.5 years ago by ▴ 50
1
vote
5
replies
2.7k
views
Extracting gene list from chromosome number and location
BiomaRt R
4.5 years ago by pjsinha07 ▴ 10
0
votes
0
replies
927
views
Does a smaller value of F from PLINK --het represent higher heterozygosity?
plink
4.5 years ago by curious ▴ 890
0
votes
0
replies
1.3k
views
vg stats meaning: difference between Total alignments and Total alignments
vg graph stats
updated 4.5 years ago by 153k • written 4.5 years ago by ▴ 20
0
votes
0
replies
884
views
is there a way to define the populations i want to test in treemix fourpop and threepop functions?
threepop fourpop threemix
4.5 years ago by rturba ▴ 10
1
vote
1
reply
1.0k
views
Diamond blastx output is huge and Megan crashes upon importing
diamond
4.5 years ago by shinyi.marzano ▴ 10
0
votes
2
replies
1.2k
views
Job: Opportunity to lead bioinformatics development at a fast growing, well-funded startup
NGS R python
updated 4.2 years ago by 45k • written 4.5 years ago by • 0
0
votes
2
replies
1.6k
views
Issues downloading fastq data
fastq-dump parallel SRA
4.5 years ago by pablojosegiraudi • 0
0
votes
0
replies
807
views
How to calculate differential coverage between two groups?
differential bed bam rnaseq coverage
4.5 years ago by O.rka ▴ 750
1
vote
3
replies
1.2k
views
Variant analysis for target NGS sequencing data?
NGS Variants
updated 2.3 years ago by 45k • written 4.5 years ago by ▴ 590
1
vote
3
replies
6.7k
views
ICE normalization using JuicerTools
Hi-C genome 3c juicer cooler
updated 4.4 years ago by ▴ 380 • written 4.7 years ago by ▴ 10
0
votes
0
replies
731
views
limma dream giving error message 'subscript out of bounds'
error Dream R
4.5 years ago by RNAseqer ▴ 280
1
vote
17
replies
4.3k
views
How to align single end multiple lane data using Hisat2?
lanes Single reads
updated 4.5 years ago by 45k • written 4.5 years ago by • 0
0
votes
0
replies
1.3k
views
Error when making TxDb object from gtf file
gtf Xenopus RStudio TxDb
4.5 years ago by bowden • 0
1
vote
1
reply
1.2k
views
Maker2 CDS outside of gene in GFF3
maker gff3
updated 4.5 years ago by 9.3k • written 4.5 years ago by • 0
2
votes
3
replies
4.4k
views
Hi-C contact probability
hi-c
updated 4.5 years ago by • 0 • written 8.5 years ago by ▴ 490
1
vote
1
reply
1.1k
views
cannot see variations on graph image
vg
updated 4.5 years ago by ▴ 550 • written 4.5 years ago by ▴ 10
0
votes
2
replies
1.2k
views
No sample in the VCF file!
VCF VCFR
updated 4.5 years ago by 45k • written 4.5 years ago by • 0
12
votes
16
replies
3.8k
views
6 follow
How to extract specific fasta files ?
fasta DNA alignment RNA
updated 4.5 years ago by 21k • written 4.5 years ago by ▴ 1000
8
votes
4
replies
3.5k
views
Snakemake wildcard usage
Snakemake
4.5 years ago by devon.orourke ▴ 50
0
votes
0
replies
967
views
Job: Bioinformatician position in RNA biology - Eric Lai lab, MSKCC, NYC
m6A miRNA APA RNA
4.4 years ago by laie ▴ 10
0
votes
0
replies
558
views
Question about Four Russians speed up for block alignment and longest common subsequence.
Sequence_Alignment
4.5 years ago by KangarooChief • 0
6
votes
16
replies
5.4k
views
6 follow
Grep specific sequence
fastq smallRNA_Seq smallRNA GREP
updated 4.5 years ago by 56k • written 4.5 years ago by • 0
3
votes
3
replies
1.7k
views
how to intersect two files based on three columns
python awk bash
updated 4.5 years ago by 11k • written 4.5 years ago by ▴ 320
19
votes
10
replies
16k
views
7 follow
Automatic Outlier Detection for RNA-seq data
RNA-Seq outlier rrcov
updated 4.0 years ago by ▴ 130 • written 7.9 years ago by ▴ 760
11
votes
20
replies
8.6k
views
Comparing Two Fastq Files Linux
illumina genomics
updated 4.2 years ago by 45k • written 4.5 years ago by ▴ 70
0
votes
7
replies
2.5k
views
remove unmapped reads on a specific chromosome only
bam remove unmapped
updated 4.5 years ago by 22k • written 4.5 years ago by ▴ 320
0
votes
0
replies
1.1k
views
Active regions determination in HaplotypeCaller
SNP GATK VCF HaplotypeCaller BAM
4.5 years ago by Nawar • 0
2
votes
1
reply
1.0k
views
Plot SNPs on transcripts
transcripts SNP gene plot
updated 4.5 years ago by 7.9k • written 4.5 years ago by ▴ 10
0
votes
0
replies
913
views
A question about analyzing MACS2 outputs
broad-peak dropa drip-seq macs2
4.5 years ago by Bertalan_Takacs ▴ 140
0
votes
0
replies
1.0k
views
Copy number Variation frequency plot
CNV EPIC 450k methylation
4.5 years ago by user911111111 • 0
0
votes
1
reply
1.3k
views
DiffBind - dba.report concentration value question
DiffBind
updated 4.5 years ago by ★ 2.1k • written 4.5 years ago by ▴ 30
0
votes
1
reply
956
views
How to generate bam files containing the entire read alignments?
bam RNAseq reads alignment
updated 4.5 years ago by 9.0k • written 4.5 years ago by • 0
18
votes
4
replies
32k
views
6 follow
Volcano plot p-value or FDR?
RNA-Seq
updated 4.5 years ago by 15k • written 9.4 years ago by ▴ 80
1
vote
1
reply
1.2k
views
scRNA sequence compare between conditions and get differentially expressed genes
Seurat scRNA R
updated 4.5 years ago by ★ 1.7k • written 4.5 years ago by ▴ 20
0
votes
1
reply
1.2k
views
Multiple Transctipr ID (NM ) from MyVariantInfo
snp transcript dna-seq
updated 4.5 years ago by ▴ 720 • written 4.5 years ago by ▴ 200
0
votes
0
replies
870
views
WGCNA
screening network
4.5 years ago by artepapa • 0
1
vote
0
replies
838
views
sc-ATAC UMIs
sc-RNA scATAC NGS UMIs sc-ATAC
4.5 years ago by scrnaresearch ▴ 10
1
vote
4
replies
1.9k
views
Finding transcriptome coverage of genome
mapping transcriptome trinity RNAseq
updated 4.5 years ago by ▴ 720 • written 4.5 years ago by ▴ 40
121,906 results • Page 677 of 2439
Recent Votes
Answer: Tried building a compact sequence format with 4-bit storage
Tried building a compact sequence format with 4-bit storage
Shift in RNA 3' position, Term-Seq vs RNASeq
Comment: STARlong for pacbio Isoseq reads
Comment: Automatically annotating a feature using a genbank file
Answer: Is this PCA plot correct??
Answer: Is this PCA plot correct??
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Recent Replies
Comment: Is total miRNA in EV constant? Implications for library size normalization. by Gordon Smyth ★ 8.3k
RNA-seq is very good at relative analyes. It would be straightforward to determine which miRNAs are relatively more abundant, compared to o…
Comment: Tried building a compact sequence format with 4-bit storage by Pranava ▴ 10
Woah!!! Thank you very much, Matthias. I honestly didn't even know some of those existed and I will definitely go through them and try to u…
Answer: Tried building a compact sequence format with 4-bit storage by Matthias Zepper 5.1k
Hello Pranava, Thanks for sharing your repository. Devising a new file format is an interesting undertaking and certainly a task with many…
Answer: Gene Ontology Enrichment with LOC gene IDs in Common Carp (Cyprinus carpio) by GenoMax 153k
`LOC` gene ID's are often assigned to uncharacterized genes and you may not get useful information from databases for them, thus they will …
Comment: Whole Genome Sequencing IG regions by GenoMax 153k
> are the calls I am seeing reliable or should I take them with something of a pinch of salt? Not sure what calls you are referring to but…
Comment: RNA-SEQ where only a subset of genes is of interest by piffelpaff • 0
Sorry to revive this ancient thread but I'm currently discussing the same question with some people in my lab and would love to somebody po…
Answer: STARlong for pacbio Isoseq reads by YuZJ • 0
Hello, you may try deSALT (DOI: 10.1186/s13059-019-1895-9, GitHub: ydLiu-HIT/deSALT) or uLTRA (DOI: 10.1093/bioinformatics/btab540, GitHub:…
Comment: Shift in RNA 3' position, Term-Seq vs RNASeq by acvill ▴ 350
Without knowing the details of the Term-seq method, could the 38 nt shift be accounted for by the difference in the position of the ribosom…
Comment: STARlong for pacbio Isoseq reads by Buffo ★ 2.4k
Thanks, I'll give it a try.
Comment: STARlong for pacbio Isoseq reads by GenoMax 153k
You could give `mapPacBio.sh` from BBMap suite a try while you wait for other answers. That works for reads up to 6 kb. BBMap has a new hom…
Comment: STARlong for pacbio Isoseq reads by Buffo ★ 2.4k
The average is 1.8kb. I was planning to post it on GitHub, but it seems like the repository has been unattended for the last months, so I d…
Comment: Getting just fastqc.zip file? by GenoMax 153k
Yes, You can either use it on command line or use the graphical user interface.
Comment: STARlong for pacbio Isoseq reads by GenoMax 153k
What is the average length of your reads? That error sounds like a bug, so you may want to post that on `STAR` repo as an issue. I assume …
Comment: Getting just fastqc.zip file? by pourhangleila95 • 0
I want to perform fastQC on my data.Do you use fastQC software for doing it?
Comment: Whole Genome Sequencing IG regions by 719 • 0
Sorry for the poor wording of the original post, also should say I really appreciate people taking a moment to look at my post. My main con…
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