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34 results • Page
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4
views
How to calculate the Z value of infernal cmscan?
cmscan
ncRNA
infernal
8 minutes ago by
shelvenlone
• 0
0
votes
2
replies
14
views
how to get pfam id of proteins belonging to a particular family along with sequences in that family?
pfam
protein
id
interpro
sequence
updated 12 minutes ago by
GenoMax
126k • written 20 minutes ago by
max
• 0
0
votes
0
replies
3
views
Converting Abricate output (.tsv) to gff3 format
gff3
convert
tsv
Abricate
10 minutes ago by
ghataksnd
▴ 10
0
votes
0
replies
17
views
samtools mpileup - bases string explanation
samtools
mpileup
58 minutes ago by
igorm
▴ 20
0
votes
2
replies
32
views
samtools idxstats not removing ChrM
samtools
ChIPseq
updated 20 minutes ago by
benformatics
3.4k • written 1 hour ago by
Jen
▴ 40
0
votes
3
replies
365
views
Practical Haplotype Graph -- Pathing Error
PHG
updated 1 hour ago by
lcj34
▴ 220 • written 25 days ago by
wcs98
• 0
0
votes
2
replies
64
views
Problem in converting SAM to BAM file by DROP SEQ
SAMtoBAM
updated 20 minutes ago by
benformatics
3.4k • written 3 hours ago by
VANSHIKA
• 0
0
votes
2
replies
92
views
Trying to install Roary with Conda results in error message
error
roary
conda
2 hours ago by
tobiwan
• 0
0
votes
2
replies
76
views
UnicodeDecodeError: 'utf-8' codec can't decode byte 0x8b in position 1: invalid start byte
vcf.gz
UnicodeDecodeError
ancIBD
3 hours ago by
wangjincheng
• 0
1
vote
1
reply
178
views
What is the difference between agilent_wholegenome and agilent_wholegenome_4x44k_v1 in biomart?
bioinformatics
biomaRt
biomart
genetics
gene
updated 4 hours ago by
Mike Smith
★ 2.0k • written 1 day ago by
solarchan7
• 0
0
votes
0
replies
71
views
got error while running Virusfinder, Please find the attached image for the details of the error, also blat_out_candidate_singlelane.fa is 0 in size.…
Step2
Virusfinder
4 hours ago by
DC
• 0
5
votes
3
replies
248
views
Where do find virulence gene information in a gff/gtf file?
microbial
genomics
gff
annotation
gtf
updated 4 hours ago by
oschwengers
▴ 90 • written 1 day ago by
sovrappensiero
▴ 60
7
votes
6
replies
307
views
6 follow
split fasta file to train deep learning model
fasta
split
bash
R
updated 3 hours ago by
shenwei356
7.9k • written 17 hours ago by
pinheirofabiano
▴ 10
0
votes
0
replies
75
views
Fine mapping with GWAS
PAINTOR
GWAS
FINE-MAP
POST-GWAS
updated 3 hours ago by
Nicolas Rosewick
10k • written 6 hours ago by
Swati
• 0
0
votes
2
replies
135
views
GIAB Truth Set
GIAB
5 hours ago by
sheryl
▴ 180
0
votes
0
replies
75
views
How would I assess evolutionary estimates between duplicated vs. non-duplicated genes in PAML?
PAML
12 hours ago by
codoncity
• 0
2
votes
2
replies
172
views
FastQ file not recognized by hisat2 allignment
hisat2
rnaseq
rna-seq
nextflow
updated 4 hours ago by
Maxime Garcia
▴ 220 • written 14 hours ago by
selenaajohn
• 0
1
vote
2
replies
154
views
FeatureCounts >edgeR > GO
RNA-SEQ
14 hours ago by
Pegasus
▴ 80
2
votes
2
replies
1.8k
views
BWA alignment score calculation
score
SAM
BWA
alignment
updated 17 hours ago by
kmzhou4
• 0 • written 21 months ago by
Donovan
▴ 20
0
votes
5
replies
484
views
Bad quality fastq files for analysis
quality
bad
DNA-seq
fastq
alignment
updated 20 hours ago by
GenoMax
126k • written 2 days ago by
Gene_MMP8
▴ 220
0
votes
0
replies
101
views
TCGA Methylation Data and Gene Mapping
Methylation
Cancer
TCGA
21 hours ago by
James
▴ 30
1
vote
2
replies
179
views
Handling single-sample VCF after haplotypecaller
VCF
12 hours ago by
Y.H.P
• 0
0
votes
0
replies
99
views
MethylR on bam files Gives Error
MethylR
bismark
22 hours ago by
anasjamshed
▴ 120
1
vote
2
replies
256
views
Human Population Reference Genomes (+Neanderthal?)
comparative
genomics
15 hours ago by
emm008
• 0
0
votes
1
reply
174
views
just one plot appears in the shiny application not all
plot
source
shiny
code
updated 14 hours ago by
bkleiboeker
▴ 310 • written 1 day ago by
mrashad
▴ 60
0
votes
2
replies
185
views
Nextflow Stringtie: command not found Error
nextflow
rna-seq
stringtie
updated 1 hour ago by
ATpoint
70k • written 1 day ago by
selenaajohn
• 0
0
votes
0
replies
195
views
Simes method
simes
method
SNP
R
7 hours ago by
Eliza
▴ 10
5
votes
6
replies
409
views
Nextflow: No space left on device, process using output directory as input?
nextflow
updated 2 hours ago by
Maxime Garcia
▴ 220 • written 2 days ago by
Eliveri
▴ 320
2
votes
4
replies
447
views
msigdbr returns the same genesets for mouse as in for human,
msigdbr
14 hours ago by
e.r.zakiev
▴ 30
4
votes
7
replies
498
views
Calculate RPKM
RPKM
12 hours ago by
Chris
▴ 70
5
votes
3
replies
340
views
News:
March 13-16: Virtual Nextflow and nf-core training event in 5 languages
nf-core
pipeline
Nextflow
updated 4 hours ago by
Maxime Garcia
▴ 220 • written 4 weeks ago by
Matthias Zepper
3.3k
3
votes
7
replies
2.2k
views
7 follow
Converting an output de-novo transcriptome assembled with Trinity to a .gff3 file
Trinity
updated 1 hour ago by
EkHe
• 0 • written 3.5 years ago by
Raito92
▴ 80
3
votes
8
replies
5.7k
views
Help with designing limma contrast matrix
limma
software error
updated 21 hours ago by
Kevin Blighe
84k • written 5.0 years ago by
fi1d18
★ 4.1k
25
votes
13
replies
25k
views
8 follow
Bowtie2 parameters for best alignment
alignment
Assembly
genome
SNP
updated 13 hours ago by
kalavattam
▴ 90 • written 8.8 years ago by
cvu
▴ 180
34 results • Page
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Recent Votes
Answer: What is the difference between agilent_wholegenome and agilent_wholegenome_4x44k
C: Converting an output de-novo transcriptome assembled with Trinity to a .gff3 fil
unplaced, unlocalized, ... scaffolds from hg19 to GRCh38
C: extracting heterozygous snp from a vcf file
Comment: March 13-16: Virtual Nextflow and nf-core training event in 5 languages
Answer: Where do find virulence gene information in a gff/gtf file?
Comment: split fasta file to train deep learning model
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Recent Replies
Answer: how to get pfam id of proteins belonging to a particular family along with seque
by
GenoMax
126k
Visit: https://www.uniprot.org/uniprotkb?query=(taxonomy_id:9606) Click on `customize columns`. Search with keyword `pfam` and check the…
Comment: how to get pfam id of proteins belonging to a particular family along with seque
by
Pierre Lindenbaum
153k
use the data in the download section ? $ wget -qO - "https://ftp.ebi.ac.uk/pub/databases/interpro/current_release/protein2ipr.dat.gz" …
Comment: Problem in converting SAM to BAM file by DROP SEQ
by
benformatics
3.4k
i think picard is expecting read groups. you may need to add them: https://gatk.broadinstitute.org/hc/en-us/articles/360037226472-AddOrRepl…
Comment: samtools idxstats not removing ChrM
by
benformatics
3.4k
i'm not sure this is doing what you expect? you should try filtering your bam directly and then running idx stats samtools view -h yo…
Comment: samtools idxstats not removing ChrM
by
Jeremy Leipzig
21k
can we see the output from this? `samtools idxstats chipseq/results/bowtie2/PPARg/PPARg_Input_Rep1_aln_sorted.bam` conversely just as an e…
Comment: Nextflow Stringtie: command not found Error
by
ATpoint
70k
It's bad practice to delete posts that received an answer ( = a user invested time - in this case me but it of course applies generally). D…
Comment: Converting an output de-novo transcriptome assembled with Trinity to a .gff3 fil
by
EkHe
• 0
Hi @juke34, if you're able, can you please clarify something for me (based on the answer you've given here)? Thanks a lot in advance. I als…
Answer: Practical Haplotype Graph -- Pathing Error
by
lcj34
▴ 220
FYI - The latest PHG docker version (tag 1.4) has a fix for this issue.
Comment: Nextflow: No space left on device, process using output directory as input?
by
Maxime Garcia
▴ 220
Nextflow should only link inputs (unless stated otherwise), so even if you use outdir as input it should not be much of an issue, but still…
Comment: Problem in converting SAM to BAM file by DROP SEQ
by
lieven.sterck
14k
Hi https://www.biostars.org/u/126271/, welcome. it might be good to add some more info on your "question". Now it only shows an error mes…
Comment: Trying to install Roary with Conda results in error message
by
tobiwan
• 0
Thank you for your answer I'm using Ubuntu 22.04.2 LTS, command line used: conda install roary. Or do you need a screenshot of the whole …
Comment: Nextflow: No space left on device, process using output directory as input?
by
colindaven
4.5k
Yes, don't use the outdir as an input. You might get infinite loops.
Comment: UnicodeDecodeError: 'utf-8' codec can't decode byte 0x8b in position 1: invalid
by
wangjincheng
• 0
I tried unzipped file, it shows the same error
Comment: UnicodeDecodeError: 'utf-8' codec can't decode byte 0x8b in position 1: invalid
by
Pierre Lindenbaum
153k
> use python package to load and analysis vcf.gz files looks like it doesn't like gzipped file. Are you sure this software can read gzip…
Comment: Trying to install Roary with Conda results in error message
by
ATpoint
70k
This cannot be answered. Add your command line and operating system.
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