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1,000 results • Page
2 of 20
Sort: replies
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Views
Votes
Replies
9
votes
20
replies
3.2k
views
Solve SAM issues flagged by Picard's ValidateSamFile
Picard
SAM file
alignment error
4.6 years ago by
marongiu.luigi
▴ 670
6
votes
20
replies
5.4k
views
filling of missing genotype information in merged variant call vcf file
SNP
4.8 years ago by
princy149
▴ 80
8
votes
20
replies
1.7k
views
Getting read depth for normal and tumour
R
WGS
vcf
4.0 years ago by
fi1d18
★ 4.1k
8
votes
20
replies
1.8k
views
Converting runpsipred Script to Work on Windows OS
psipred
windows
updated 10 months ago by
Ram
38k • written 4.7 years ago by
Bara'a
▴ 270
4
votes
20
replies
1.1k
views
How can I count aminoacid residues from a HUGE compressed fasta file?
sequence
3.2 years ago by
schlogl
▴ 130
22
votes
20
replies
2.0k
views
what is the prefered strategy to treat with blast-less transcriptomes from RNA-seq
RNA-Seq
blast
gene
genome
Forum
6.7 years ago by
Farbod
★ 3.4k
5
votes
20
replies
7.3k
views
How to plot ChIP-seq Density vs Distance from TSS using Homer annoted files
ChIP-Seq
homer
6.6 years ago by
varsha619
▴ 90
8
votes
20
replies
2.2k
views
Why does cufflinks split this transcript?
RNA-Seq
cufflinks
assembly
5.2 years ago by
corend
▴ 70
6
votes
19
replies
2.1k
views
Clustering for Single-cell RNA-seq Data
clustering
R
single-cell
3.6 years ago by
aloke205
▴ 40
18
votes
19
replies
1.6k
views
6 follow
Extremely important marker gene has many reads based on IGV viewer but no quantified reads
rna-seq
sequencing
igv
alignment
next-gen
updated 3 months ago by
Ram
38k • written 4.2 years ago by
rbkh09
• 0
10
votes
19
replies
2.4k
views
What is a difference between uniprot and 'nr. Non-redundant GenBank...'?
Genebank
blast
UniProt
updated 22 months ago by
GenoMax
127k • written 22 months ago by
matt
▴ 20
0
votes
19
replies
1.1k
views
map fasts files
RNA-Seq
FASTQ
R
5.1 years ago by
Learner
▴ 260
3
votes
19
replies
4.6k
views
gatk-launch file missing
next-gen
sequencing
software error
updated 3.9 years ago by
finswimmer
16k • written 3.9 years ago by
sruthi
▴ 40
0
votes
19
replies
3.2k
views
Difficulty installing GATKtoolkit
GATK
Variant calling
SNPs
Indels
5.2 years ago by
jaqx008
▴ 110
9
votes
19
replies
1.6k
views
There are any way to use a script for feed emboss with fasta sequence?
sequence
3.2 years ago by
schlogl
▴ 130
4
votes
19
replies
2.4k
views
Use machine learning as classifier
R
rRNA
16S
18S
ITS
updated 5.6 years ago by
Biostar
20 • written 5.7 years ago by
cool.abbecker
▴ 30
7
votes
19
replies
6.3k
views
[R] Microarray analysis interpreting logFC after makeContrasts
microarray
R
updated 13 months ago by
Ram
38k • written 8.4 years ago by
mheiser1
▴ 10
7
votes
19
replies
2.3k
views
mapping script process sleeping on server.
alignment
updated 10 months ago by
Ram
38k • written 8.0 years ago by
lvogel
▴ 30
0
votes
19
replies
7.9k
views
Skip orientation as there are not enough pairs by bwa mem
whole genome
bwa
paired end sequencing
3.8 years ago by
seta
★ 1.8k
13
votes
19
replies
4.2k
views
bbmerge not joining paired-end reads
bbmerge
alignment
5.3 years ago by
bioplanet
▴ 60
1
vote
19
replies
1.5k
views
High no feature counts in ht-seq counts
RNA-Seq
sequencing
4.3 years ago by
eozcan
▴ 10
5
votes
19
replies
1.3k
views
how I can come up with a permanent error
R
software error
5.9 years ago by
fi1d18
★ 4.1k
17
votes
19
replies
2.1k
views
Sorting sequences according header
software error
sequence
Assembly
next-gen
6.6 years ago by
Gian77
▴ 60
6
votes
19
replies
1.2k
views
Fastq header modification
sequence
next-gen
updated 5.0 years ago by
Ram
38k • written 5.0 years ago by
Guillaume
• 0
0
votes
19
replies
1.0k
views
scatterplot in R
microarray
expression
gene
updated 5 months ago by
Ram
38k • written 5 months ago by
bioinformatics
▴ 10
1
vote
19
replies
5.6k
views
Conda install package - different internals
R
software error
updated 3.6 years ago by
Biostar
20 • written 3.6 years ago by
lihe.liu
▴ 30
0
votes
19
replies
976
views
best blast strategy: read vs cluster?
alignment
blast
search
strategy
3.3 years ago by
marongiu.luigi
▴ 670
15
votes
19
replies
1.3k
views
trimmomaric command for a fasta file?
trimmomatic
updated 4.9 years ago by
Ram
38k • written 4.9 years ago by
Nadin.asal
• 0
0
votes
19
replies
2.0k
views
error related to vcfstats
numpy
snp
vcf
vcfstats
19 months ago by
rheab1230
▴ 140
22
votes
19
replies
2.4k
views
targets of a list of miRNAs
miRNAs
RNA-Seq
DEanalysis
target-prediction
6.5 years ago by
fi1d18
★ 4.1k
2
votes
18
replies
5.2k
views
No differentially expressed genes using DESeq2
RNA-Seq
deseq2
6.3 years ago by
Sumit Paliwal
▴ 40
2
votes
18
replies
1.7k
views
I need help in this
gene
weblems
alignment
updated 7 months ago by
Ram
38k • written 7.2 years ago by
efosa15
• 0
4
votes
18
replies
12k
views
Alignment with BWA and SAMtools
BWA
SAM-file
SAMtools
updated 2.4 years ago by
Biostar
20 • written 4.6 years ago by
Shelle
▴ 30
3
votes
18
replies
1.9k
views
Help creating Deseq2 count matrix from separate files
or
Sample
matrix
updated 20 months ago by
Ram
38k • written 20 months ago by
Nai
▴ 50
7
votes
18
replies
3.9k
views
Fold change UP and Down in dplyr calculation
R
5.6 years ago by
krushnach80
★ 1.1k
3
votes
18
replies
895
views
6 follow
What sequencing/alignment artifact is this?
variants
mutect
sequencing
alignment
mitochondria
4 months ago by
lacb
▴ 120
14
votes
18
replies
4.1k
views
GATK Haplotype Caller
next-gen
GATK
haplotype
caller
contigs
updated 6.2 years ago by
Biostar
20 • written 6.4 years ago by
plink_9857
▴ 50
4
votes
18
replies
3.3k
views
Significance of reads mapping to Viruses - FusionCatcher
RNA-Seq
virus
reads
fusion
updated 7 months ago by
Ram
38k • written 7.3 years ago by
Joel TM
▴ 60
7
votes
18
replies
7.6k
views
9 follow
Cuffmerge running error
RNA-Seq
updated 13 months ago by
Ram
38k • written 8.4 years ago by
hana
▴ 190
5
votes
18
replies
4.9k
views
EnhancedVolcano plot error: Log2foldchange is not numeric!
R
EnhancedVolcano
3.3 years ago by
michelle.piquet
▴ 60
0
votes
18
replies
1.2k
views
freebayes error variant calling
snp
2.6 years ago by
evelyn
▴ 220
4
votes
18
replies
2.5k
views
Inline barcodes in the reverse reads
barcodes
6.4 years ago by
Picasa
▴ 630
1
vote
18
replies
1.1k
views
Find tissues that are functionally related
tissue
functionally-related
gene-expression
updated 3.5 years ago by
Biostar
20 • written 3.6 years ago by
Natasha
▴ 40
1
vote
18
replies
2.1k
views
Why big gaps when I use Entrez Eutils to download protein coding sequences.
entrez
eutils
6.6 years ago by
Tom
▴ 40
7
votes
18
replies
3.9k
views
Bowtie indexing of a fasta file that consists of a large amount of sequences
bowtie
alignment
genome
6.4 years ago by
valerie
▴ 100
16
votes
18
replies
3.8k
views
8 follow
Python Program to read .fasta file to .txt file
Python
updated 3.6 years ago by
Mensur Dlakic
★ 23k • written 3.6 years ago by
tikshyadav19
• 0
2
votes
18
replies
1.7k
views
Bwa on multiple processor
np
mpirun
bwa
alignment
14 months ago by
shivangi.agarwal800
▴ 120
0
votes
18
replies
954
views
No gene name after annovar vcf file processing
vcf
annovar
3.4 years ago by
valerie
▴ 100
14
votes
17
replies
4.9k
views
HiSeq 4000 PhiX screening and removal using bbduk
spikein
filtering
bbmap
bbduk
phix
5.6 years ago by
Anand Rao
▴ 550
0
votes
17
replies
1.0k
views
Transcripts with no read support
RNA-Seq
alignment
assembly
salmon
2.5 years ago by
Dunois
★ 2.3k
1,000 results • Page
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Comment: Where do find virulence gene information in a gff/gtf file?
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Comment: Can I use abundance from Tximport to compare the expression level of transcript
by
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38k
Oh, you can just use TPM to do that. Within sample comparison is a completely different (and much easier) game.
Comment: ClusterProfiler enrichKEGG – remove organism name in plots?
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Comment: getting coding exon information from Ensembl API
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Because you just answer when it's a stupid question or when I ask a lot of questions. This is for asking questions not for being judged by …
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Thanks, I am not doing any differential. But, Can we say that 6th transcript is relatively more abundance in our sample than other transcri…
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It looks like the ImputePipelinePlugin for the minimap2 run does not use the numThreads Option but rather does the numThreadsOnMachine - 2 …
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@rob Please, Can you or people from your group answer . As I am using one of your paper as my [reference.][1] [1]: https://f1000rese…
Comment: fastq_screen error: Failed to calculate read length
by
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★ 1.5k
I created the .fasta from a BAM, so I am just going to go back to the BAM and convert that to a .fastq and see if that works. But good to k…
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You could use `bedmap` from BEDOPS. Say you have a BED file of IS/transposable elements called `elements.bed` and a BED file of genes calle…
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Hello, Thank you. An explanation of where I came up with 2500 is 10 million divided by 1000 (because sample freq is 1000), divided again b…
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You can run PCA yourself with only few lines of code. See here under PCA https://www.biostars.org/p/461026/ You can then use the prcomp ou…
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