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83 results • Page
1 of 2
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Views
Votes
Replies
15
votes
16
replies
818
views
ncbi error report log for validate fastq issue
sra-tools
updated 6 days ago by
GenoMax
135k • written 6 days ago by
1769mkc
★ 1.1k
3
votes
15
replies
566
views
How to subset large BAM files specifically/ extract specific subsets?
bamtools
RNAseq
samtools
BAM
5 days ago by
ella
• 0
2
votes
10
replies
2.8k
views
6 follow
Split plink files by a number of SNPs
GWAS
SNP
plink
updated 5 days ago by
Raygozak
★ 1.4k • written 5.2 years ago by
kakukeshi
▴ 80
0
votes
10
replies
246
views
Rockhoppper - Suspiciously low percentage of perfectly aligned reads
Rockhopper
RNA-seq
2 hours ago by
langziv
▴ 50
0
votes
9
replies
234
views
Deseq2 error
R
deseq2
4 hours ago by
sgadila
• 0
1
vote
7
replies
3.6k
views
Adjust width of annotations in pheatmap
R
heatmap
updated 2 days ago by
Kevin Blighe
86k • written 4.9 years ago by
divya.nandakumar
▴ 30
2
votes
7
replies
707
views
Weirdness in annotation (missing allele frequencies)
allele-frequency
gnomad
annovar
updated 1 day ago by
Ram
40k • written 11 days ago by
Can Abdullah
• 0
2
votes
6
replies
269
views
Match variants from RNAseq with known databases
dbsnp
SNP
vcf
bcftools
RNA-seq
1 day ago by
dilokef367
• 0
1
vote
6
replies
722
views
18S sequence not matching 18S sequence in assembly
18S
BLAST
updated 1 day ago by
Ram
40k • written 3.2 years ago by
kristina.mahan
▴ 160
0
votes
6
replies
854
views
Illumina reads mapped back onto contigs have gaps
illumina
updated 1 day ago by
Ram
40k • written 3.0 years ago by
kristina.mahan
▴ 160
4
votes
6
replies
395
views
Hisat2 index and alignment question
ubuntu
rna-seq
index
hisat2
updated 6 days ago by
Istvan Albert
98k • written 10 days ago by
Athena
• 0
1
vote
5
replies
402
views
Complex multifactorial DE analysis with limma/edgeR based on rnaseq data
R
edgeR
limma
RNA-seq
updated 4 days ago by
LChart
3.4k • written 6 days ago by
svlachavas
▴ 780
0
votes
5
replies
1.3k
views
What Coverage allele-fraction threshold to use?
allele-fraction
snps
updated 1 day ago by
Ram
40k • written 2.5 years ago by
kristina.mahan
▴ 160
8
votes
5
replies
365
views
Frustrated with DEA results
microarray
differential-expression
updated 5 days ago by
dsull
★ 4.8k • written 6 days ago by
jopadrosa
• 0
1
vote
5
replies
299
views
CollectRnaSeqMetrics (Picard) output to convert FeatureCounts into TPM
R
Picard
CollectRnaSeqMetrics
updated 5 days ago by
Ram
40k • written 6 days ago by
camillab.
▴ 140
1
vote
4
replies
409
views
How to perform hypothesis testing on contingency tables and compare with the null distribution?
hypothesis-testing
contingency-table
4 days ago by
RK
• 0
2
votes
4
replies
3.3k
views
Converting different annotation file formats (GTF/GFF/BED) to each other
rna-seq
next-gen
updated 50 minutes ago by
alejandrogzi
▴ 30 • written 6.0 years ago by
Javad
▴ 150
0
votes
4
replies
286
views
Sequence quality drops in the 3' end of the left sequence in paired end. What could be the cause?
sequencing
updated 6 days ago by
GenoMax
135k • written 6 days ago by
eggrandio
▴ 40
0
votes
4
replies
115
views
Understanding mother and father alleles in VCF file
snp
vcf
3 hours ago by
c.
• 0
1
vote
4
replies
253
views
How to filter vcf file by MAF using bcftools?
bcftools
vcf
updated 6 days ago by
Ram
40k • written 6 days ago by
_quantum_girl_
▴ 10
0
votes
4
replies
196
views
counting from a single BAM file with multiple samples
cell-barcode
RNA-seq
updated 1 day ago by
LChart
3.4k • written 1 day ago by
dr-device
• 0
1
vote
3
replies
962
views
How to reduce Quast stats being based on "contigs of size > 100000 bp"
quast
updated 1 day ago by
Ram
40k • written 3.1 years ago by
kristina.mahan
▴ 160
3
votes
3
replies
284
views
Clustering in single cell
seurat
single-cell
5 days ago by
Chris
▴ 200
1
vote
3
replies
280
views
comparision of umap single cell
single-cell
5 days ago by
synat.keam
▴ 80
1
vote
3
replies
333
views
How to determine the total count for each gene in lymphotype B
scRNAseq
Seurat
5 days ago by
dalibenam64
• 0
0
votes
3
replies
287
views
QC of genetic data
PLINK
updated 7 hours ago by
bk11
★ 1.4k • written 4 days ago by
kl
▴ 10
0
votes
3
replies
195
views
Bug of vg surject
vg
updated 6 days ago by
Jordan M Eizenga
▴ 360 • written 6 days ago by
Qi
• 0
0
votes
3
replies
223
views
What is the correct procedure to generate a consensus bacterial sequence?
consensus
samtools
illumina
fastq
4 days ago by
marongiu.luigi
▴ 690
0
votes
3
replies
726
views
to annotate BEDPE files
bedtools
annotate
updated 6 days ago by
Lhl
▴ 760 • written 2.6 years ago by
Bogdan
★ 1.4k
1
vote
3
replies
286
views
differences between trajectories in conditions with Monocle3 or other tools
trajectory
scRna-seq
monocle3
single-cell
updated 4 days ago by
Amitm
★ 2.2k • written 4 days ago by
Chironex
▴ 40
0
votes
2
replies
197
views
Detect STRs in illumina library
repeats
annotation
STR
5 days ago by
kirillkirilenko
▴ 20
0
votes
2
replies
882
views
RSEM not giving .genes.results and isoforms.results ; Plase check if you provide correct parameters/options for the pipeline!
genomics
transcriptome
rsem
ngs
5 days ago by
kat.bi
• 0
2
votes
2
replies
293
views
bedtools intersect by position & stand not working even with common regions
bedtools
genomic
intersect
bedops
intervals
1 day ago by
Alewa
▴ 140
0
votes
2
replies
246
views
Quality Control of VCFs that used different genotyping arrays
bcftools
VCF
1 day ago by
Shane
• 0
1
vote
2
replies
302
views
functional analysis
16S
metabarcoding
functionalanalysis
1 day ago by
safeassli
• 0
0
votes
2
replies
1.1k
views
Blobtools output files
blobtools
updated 1 day ago by
Ram
40k • written 3.0 years ago by
kristina.mahan
▴ 160
2
votes
2
replies
1.9k
views
Plotting Allele Frequencies
variant-analysis
updated 1 day ago by
Ram
40k • written 4.2 years ago by
kristina.mahan
▴ 160
1
vote
2
replies
3.2k
views
rna-seq analysis with Salmon - how to Import and summarize using tximport
RNA-Seq
salmon
tximport
updated 1 day ago by
camillab.
▴ 140 • written 4.1 years ago by
woojoy14
▴ 10
1
vote
2
replies
186
views
extract first and last n bp from fasta file from multiple fasta file in R
comparative-genomics
updated 1 day ago by
Ram
40k • written 1 day ago by
praasu
▴ 40
0
votes
2
replies
167
views
How can I compute energy from a protein PDB file?
pdb
protein
updated 14 hours ago by
Matthias Zepper
4.1k • written 1 day ago by
4fzcgueyp5
• 0
0
votes
2
replies
269
views
Issues with featureCounts
featurecounts
rna-seq
differential-expression
updated 12 hours ago by
biofalconch
★ 1.0k • written 4 days ago by
Aime
• 0
1
vote
1
reply
226
views
Comparing multiple RNASeq studies
RNASeq
updated 5 days ago by
Zhenyu Zhang
▴ 980 • written 5 days ago by
Luke
▴ 10
0
votes
1
reply
197
views
Issue with merging in plink and eigensoft.
Eigensoft
Eigenstrat
Plink
updated 5 days ago by
bk11
★ 1.4k • written 5 days ago by
Jd
• 0
0
votes
1
reply
1.3k
views
Convert .sqn file to .gbk
organelle
updated 1 day ago by
Ram
40k • written 2.6 years ago by
kristina.mahan
▴ 160
0
votes
1
reply
57
views
Kimura% of calcDivergenceFromAlign output
repeatlandscape
repeatmasker
3 hours ago by
睿紘
• 0
0
votes
1
reply
143
views
Calculating haplotype and nucleotide diversity with deep amplicon sequencing data
haplotype
diversity
Pegas
Arlequin
HTS_data
6 days ago by
deorugz
• 0
0
votes
1
reply
418
views
FASTQ files for 30x 1KGP of Phase 3 data
phase3
fast
1kgp
2 hours ago by
Qboy
• 0
0
votes
1
reply
180
views
Pheatmap x must be numeric
deseq2
r
pheatmap
updated 1 day ago by
Ram
40k • written 2 days ago by
Hamza
• 0
0
votes
1
reply
124
views
FEAST - Microbial Source Tracking
Source-Tracking
Microbiome
updated 1 day ago by
Ram
40k • written 1 day ago by
avinash.dhar
• 0
0
votes
1
reply
139
views
Large fold change when analyzing expression profiling from microarray
limma
DEG
RNA
updated 1 day ago by
Ram
40k • written 1 day ago by
Yibin
• 0
83 results • Page
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Answer: tensorQTL interaction issue
Answer: Script for getting summary statistic of any genome using GTF or GFF3 ?
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Comment: How do you validate and verify your pipeline's software updates?
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Answer: Exporting DEGs obtained from DESeq2
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Comment: How to get sample names and genotype for SNP in multi-sample VCF file
by
Kevin Blighe
86k
It is difficult for me to comment, as I am not too informed on your IT infrastructure. What I can say is that it would be better to run the…
Answer: Converting from BED to SAF/GFF
by
alejandrogzi
▴ 30
I recently developed [bed2gff](https://github.com/alejandrogzi/bed2gff) to quickly convert .bed files to a gff3 format, a tool written in R…
Comment: Convert bed12 to GFF
by
alejandrogzi
▴ 30
Now there is [bed2gff](https://github.com/alejandrogzi/bed2gff), if you want to work only with a gff file!
Comment: Converting different annotation file formats (GTF/GFF/BED) to each other
by
alejandrogzi
▴ 30
now there is also [bed2gff](https://github.com/alejandrogzi/bed2gff) if you want to convert .bed files to .gff3 files!
Answer: How Do I Convert From Bed Format To Gff Format?
by
alejandrogzi
▴ 30
I recently developed [bed2gff](https://github.com/alejandrogzi/bed2gff) to quickly convert .bed files to a gff3 format, a tool written in R…
Answer: tensorQTL interaction issue
by
Solal
• 0
Writing a solution for anyone interested. The issue stems from a dosage error, some variant contains only heterozygous individuals and no h…
Answer: The Biostar Handbook. A bioinformatics e-book for beginners.
by
Qboy
• 0
Great book! I love using it to help my mentees to learn bioinformatics better. It would be also fantastic to compile all other necessary Pr…
Comment: Rockhoppper - Suspiciously low percentage of perfectly aligned reads
by
langziv
▴ 50
Thanks. I'll try.
Comment: How to get sample names and genotype for SNP in multi-sample VCF file
by
avelarbio46
▴ 30
Hi! I'm trying to parallelize your code (to run on a bunch of files), but it is not working because of multiple processes spawning. Do you …
Comment: Rockhoppper - Suspiciously low percentage of perfectly aligned reads
by
GenoMax
135k
> so I don't think the genome size is available. Perhaps not for your specific strain but plenty of other Kpn genomes are available and th…
Comment: Kimura% of calcDivergenceFromAlign output
by
睿紘
• 0
For additional information, "Coverage for each repeat class and divergence (Kimura)" is also the result from calcDivergenceFromAlign.pl
Comment: Rockhoppper - Suspiciously low percentage of perfectly aligned reads
by
langziv
▴ 50
By the way, I run Rockhopper on the untrimmed files, and the full match percentage grew to 20%-30%, and there are 1552 transcripts in the u…
Comment: Rockhoppper - Suspiciously low percentage of perfectly aligned reads
by
langziv
▴ 50
Here are the total bases in 4 fastq files (after adapter removal): 1,027,852,411, 1,041,895,083, 1,121,786,520, 1,299,721,929. I just rem…
Comment: Understanding mother and father alleles in VCF file
by
c.
• 0
actually they didn't tell me which relatives were from mother side and which from father side, you are right. But how can you find related …
Comment: Rockhoppper - Suspiciously low percentage of perfectly aligned reads
by
GenoMax
135k
Correct. Data that went into the assembly.
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