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121,908 results • Page 693 of 2439
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0
votes
1
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963
views
Kraken abundances do not add up
kraken2
4.5 years ago by jsgounot ▴ 170
1
vote
1
reply
3.4k
views
Suggest vcf filtered parameter for gatk VariantFiltration
gatk4 snps
updated 4.5 years ago by ▴ 160 • written 6.3 years ago by ▴ 140
0
votes
0
replies
767
views
Run TSS predator without TEX wig libraries
RNA-Seq sequencing next-gen software error
4.5 years ago by qstefano ▴ 20
0
votes
1
reply
1.2k
views
Repeated measures in GWAS and polygenic risk scores analyses
SNP
updated 22 months ago by 12k • written 5.5 years ago by ▴ 20
0
votes
2
replies
1.9k
views
conversion of a genlight object into a genpop object
snp R
updated 2.2 years ago by • 0 • written 5.1 years ago by • 0
0
votes
1
reply
2.7k
views
KEGG Reconstruct Pathway: More Efficient Usage
Kegg Pathway genome
updated 4.5 years ago by 20 • written 8.2 years ago by • 0
1
vote
2
replies
1.3k
views
Data normalization (raw counts) and DEG analysis. Do I have a problem with my pipeline?
R RNA-Seq
4.5 years ago by Peter ▴ 20
0
votes
0
replies
1.1k
views
Is it possible to call variants using cram files?
next-gen sequencing SNP
4.5 years ago by vinayjrao ▴ 260
32
votes
34
replies
19k
views
10 follow
How To Randomly Sample A Subset Of Lines From A Bed File
bed chip-seq
updated 3.9 years ago by 45k • written 11.9 years ago by ▴ 540
1
vote
3
replies
3.6k
views
Meme/Ame - bad file error
meme ame motif
4.5 years ago by LacquerHed ▴ 30
6
votes
8
replies
2.1k
views
What does mean HHHHHH in structures?
structure protein pdb
updated 4.5 years ago by ★ 30k • written 4.5 years ago by ▴ 80
0
votes
1
reply
2.4k
views
ERROR UTR only implemented with shadow and partial or complete. Augustus
busco Augustus
updated 4.5 years ago by ▴ 80 • written 5.4 years ago by • 0
5
votes
2
replies
1.0k
views
NCBI genome stats
genome stats ncbi
updated 4.5 years ago by 153k • written 4.5 years ago by ★ 2.0k
0
votes
0
replies
1.1k
views
gromacs: RNA-Protein interaction
gromacs RNA Protein
updated 4.5 years ago by 20 • written 4.7 years ago by ▴ 10
4
votes
10
replies
2.7k
views
Importing quant.sf file to tximport
software-error tximport genome
updated 2.3 years ago by 45k • written 4.5 years ago by • 0
2
votes
2
replies
1.9k
views
Deleting text from row.names in a dataframe
RNA-Seq
4.5 years ago by salehm ▴ 10
0
votes
1
reply
1.1k
views
Docker image exceRpt pipeline help
docker small RNA seq RNAseq exceRpt
updated 4.5 years ago by ▴ 320 • written 4.5 years ago by • 0
3
votes
3
replies
1.9k
views
How to concatenate multiple fastq files (located in different directories) for each sample
RNA-Seq
updated 4.5 years ago by 13k • written 4.5 years ago by ▴ 10
0
votes
6
replies
1.8k
views
Running PHG with singularity: Error at CreatePHG_step2_addHapsFromGVCF
PHG singularity
4.5 years ago by bp • 0
2
votes
2
replies
1.4k
views
chr20_KI270871v1_alt in HG38 Broad Variant and Blacklist regions
ChIP-Seq
4.5 years ago by ahadli.farid ▴ 50
1
vote
6
replies
1.3k
views
Is it possible to get SARS-CoV-2 sequences from https://outbreak.info/?
sequence
4.5 years ago by Juke34 9.3k
0
votes
0
replies
962
views
Difference between Go terms from blast hits and Interproscan in Blast2go
blast2go GO terms Interproscan Go graph
4.5 years ago by Kash ▴ 110
0
votes
0
replies
1.0k
views
Should i calculated Nm, UQ and MD tag of bam ?
alignment bam gatk
4.5 years ago by quentin54520 ▴ 120
11
votes
5
replies
10k
views
Remove supplementary alignments from a bam file
alignment
updated 4.5 years ago by • 0 • written 5.4 years ago by ▴ 90
3
votes
5
replies
1.6k
views
outlier detcection in a given gene expression datasets
R
updated 4.5 years ago by ▴ 270 • written 4.6 years ago by ▴ 70
0
votes
0
replies
619
views
Is there a curated list of non-genetic risk factors for diseases?
text mining risk factor
4.5 years ago by JorgeVallejo ▴ 20
0
votes
0
replies
712
views
Few samples for WGCNA coex network
RNA-Seq wgcna coexpression network
4.5 years ago by ovariohisterectomia ▴ 40
4
votes
3
replies
3.0k
views
featureCounts - Low Assigned rate - Locations of reads
RNA-Seq featureCount QC
updated 4.5 years ago by 20 • written 4.6 years ago by ▴ 80
3
votes
4
replies
2.6k
views
genes underlying gseGO categories
gseGO GSEA clusterProfiler enrichPlot
4.5 years ago by LacquerHed ▴ 30
2
votes
9
replies
2.4k
views
Setup PHG with Singularity
phg
updated 4.5 years ago by • 0 • written 4.7 years ago by ▴ 20
5
votes
4
replies
2.3k
views
hmmsearch output multiple alignment with initial query sequences
hmmer hmmsearch homology
updated 4.5 years ago by ★ 30k • written 4.5 years ago by ▴ 80
1
vote
5
replies
1.7k
views
Read count using htseq-count.
Assembly RNA-Seq gene
updated 2.5 years ago by 45k • written 4.5 years ago by ▴ 10
98
votes
12
replies
64k
views
6 follow
Ensembl-Ids Vs. Entrez-Ids
ensembl entrez gene
updated 4.5 years ago by ▴ 10 • written 13.7 years ago by ▴ 420
0
votes
3
replies
2.2k
views
readVCF in PopGenome can't open VCF file
RNA-Seq R vcf
4.5 years ago by julianneradford ▴ 20
2
votes
4
replies
2.4k
views
FeatureCounts output and downstream analysis
RNA-Seq sequencing featureCounts gene DESeq2
updated 4.5 years ago by 153k • written 4.5 years ago by ▴ 10
0
votes
0
replies
641
views
Mitigating technical allelic dropout in Single cell allelic RNA seq analysis
RNA-Seq rna-seq alignment sequencing sequence
4.5 years ago by luckysardar171 ▴ 20
0
votes
2
replies
830
views
How much sequencing coverage do you need in order to detect SNP's across the whole genome
sequencing SNP ChIP-Seq next-gen
4.5 years ago by dk0319 ▴ 70
1
vote
2
replies
835
views
How could I analyse the differential expression of a particular gene with RNA-seq data?
RNA-Seq gene
updated 4.5 years ago by 15k • written 4.5 years ago by • 0
1
vote
2
replies
1.4k
views
How to generate haplotypes with SNPs from WGS ?
SNP plink haplotype
updated 4.5 years ago by 11k • written 4.5 years ago by ▴ 10
1
vote
1
reply
1.0k
views
GO analysis: Why did gene set with high cluster frequency from up-regulation category will disappear from GO analysis of all DEGs ?
GO GSEA RNA-Seq sequencing
4.5 years ago by greyman ▴ 190
0
votes
1
reply
633
views
Is there a straightforward way to use RNA alignment with the genome to infer exon-intron structure?
RNA-Seq genome alignment sequencing next-gen
4.5 years ago by charleslindberg976 • 0
149
votes
35
replies
66k
views
33 follow
Tutorial: Tools For Metagenomic Data Analysis
metagenomics next-gen
updated 2.6 years ago by 45k • written 12.8 years ago by ★ 1.6k
0
votes
1
reply
723
views
delete several ranges from a DNA sequence
genome slicing delete segments
updated 4.5 years ago by 13k • written 4.5 years ago by • 0
4
votes
2
replies
1.5k
views
TSS predator input files
RNA-Seq software error alignment
updated 4.5 years ago by ★ 2.1k • written 4.5 years ago by ▴ 20
1
vote
3
replies
21k
views
bed to vcf format conversion
bed vcf
updated 2.5 years ago by 45k • written 9.3 years ago by ▴ 10
0
votes
5
replies
4.8k
views
DEGpatterns and functional analysis of clusters
RNA-Seq DEGreport DESeq2 R
updated 4.5 years ago by 89k • written 4.5 years ago by • 0
2
votes
2
replies
1.5k
views
Diffbind-weird Fold value
ChIP-Seq
updated 4.5 years ago by ★ 2.1k • written 4.5 years ago by • 0
0
votes
0
replies
669
views
How can I download Methylation data for MethylMix package. (unusual error popped)
R software error MethylMix Methylation
4.5 years ago by shlokanegi.phe18 • 0
0
votes
0
replies
1.7k
views
Job: PhD student in precision cancer bioinformatics | Charite, Berlin, Germany
cancer berlin precision-cancer ngs
updated 2.2 years ago by 45k • written 4.5 years ago by • 0
1
vote
3
replies
1.3k
views
How do I perform MAF analysis for each family separately in PLINK?
plink family population split MAF
4.5 years ago by Alana.selli • 0
121,908 results • Page 693 of 2439
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Answer: Tried building a compact sequence format with 4-bit storage
Tried building a compact sequence format with 4-bit storage
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Recent Replies
Comment: Hifiasm is getting killed while trying to assemble a genome by pranavdatar01 • 0
Yes, I did check for adaptor contamination, and did not find any. I have kept all the reads with quality score of more than 30.
Comment: Hifiasm is getting killed while trying to assemble a genome by Panos ★ 1.8k
No overlapping reads? Have you checked for contamination?
Comment: Tried building a compact sequence format with 4-bit storage by Pranava ▴ 10
I see, but the reason I was planning on using a 4bit system is so that there wouldn't be too much data loss but thank you for the suggesti…
Comment: Splice junctions plots for long-read seq data by alison.ludzki • 0
Thank you! I will check out miso!
Comment: Hifiasm is getting killed while trying to assemble a genome by pranavdatar01 • 0
I did subsample the data to 30x coverage. I did run hifiasm on it, the log file did show some contents, but hifiasm ended again, stating th…
Comment: Tried building a compact sequence format with 4-bit storage by Alex Reynolds 36k
Using four bits for storage won't beat 2bit, of course, but direct access to a sequence of interest sounds interesting and useful and might…
Comment: Hifiasm is getting killed while trying to assemble a genome by Panos ★ 1.8k
Why don't you subsample your HiFi reads and try running hifiasm again? Maybe this will help if you have memory problems. However, I haven't…
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…
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