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34 results • Page
1 of 1
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0
votes
0
replies
10
views
samtools mpileup - bases string explanation
samtools
mpileup
13 minutes ago by
igorm
▴ 20
0
votes
1
reply
16
views
samtools idxstats not removing ChrM
samtools
ChIPseq
updated 7 minutes ago by
Jeremy Leipzig
21k • written 35 minutes ago by
Jen
▴ 40
0
votes
3
replies
363
views
Practical Haplotype Graph -- Pathing Error
PHG
updated 55 minutes ago by
lcj34
▴ 220 • written 25 days ago by
wcs98
• 0
0
votes
1
reply
47
views
Problem in converting SAM to BAM file by DROP SEQ
SAMtoBAM
updated 2 hours ago by
lieven.sterck
14k • written 2 hours ago by
VANSHIKA
• 0
0
votes
2
replies
75
views
Trying to install Roary with Conda results in error message
error
roary
conda
1 hour ago by
tobiwan
• 0
0
votes
2
replies
61
views
UnicodeDecodeError: 'utf-8' codec can't decode byte 0x8b in position 1: invalid start byte
vcf.gz
UnicodeDecodeError
ancIBD
2 hours ago by
wangjincheng
• 0
0
votes
1
reply
168
views
What is the difference between agilent_wholegenome and agilent_wholegenome_4x44k_v1 in biomart?
bioinformatics
biomaRt
biomart
genetics
gene
updated 3 hours ago by
Mike Smith
★ 2.0k • written 1 day ago by
solarchan7
• 0
0
votes
0
replies
62
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
3 hours ago by
DC
• 0
5
votes
3
replies
240
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
269
views
6 follow
split fasta file to train deep learning model
fasta
split
bash
R
updated 2 hours ago by
shenwei356
7.9k • written 16 hours ago by
pinheirofabiano
▴ 10
0
votes
0
replies
73
views
Fine mapping with GWAS
PAINTOR
GWAS
FINE-MAP
POST-GWAS
updated 2 hours ago by
Nicolas Rosewick
10k • written 6 hours ago by
Swati
• 0
0
votes
2
replies
130
views
GIAB Truth Set
GIAB
4 hours ago by
sheryl
▴ 180
0
votes
0
replies
70
views
How would I assess evolutionary estimates between duplicated vs. non-duplicated genes in PAML?
PAML
11 hours ago by
codoncity
• 0
2
votes
2
replies
153
views
FastQ file not recognized by hisat2 allignment
hisat2
rnaseq
rna-seq
nextflow
updated 3 hours ago by
Maxime Garcia
▴ 220 • written 13 hours ago by
selenaajohn
• 0
1
vote
2
replies
148
views
FeatureCounts >edgeR > GO
RNA-SEQ
13 hours ago by
Pegasus
▴ 80
2
votes
2
replies
1.8k
views
BWA alignment score calculation
score
SAM
BWA
alignment
updated 16 hours ago by
kmzhou4
• 0 • written 21 months ago by
Donovan
▴ 20
0
votes
5
replies
482
views
Bad quality fastq files for analysis
quality
bad
DNA-seq
fastq
alignment
updated 19 hours ago by
GenoMax
126k • written 2 days ago by
Gene_MMP8
▴ 220
0
votes
0
replies
99
views
TCGA Methylation Data and Gene Mapping
Methylation
Cancer
TCGA
20 hours ago by
James
▴ 30
1
vote
2
replies
175
views
Handling single-sample VCF after haplotypecaller
VCF
11 hours ago by
Y.H.P
• 0
0
votes
0
replies
97
views
MethylR on bam files Gives Error
MethylR
bismark
22 hours ago by
anasjamshed
▴ 120
0
votes
0
replies
102
views
pyscenic
pyscenic
scenic
23 hours ago by
Andy
▴ 30
1
vote
2
replies
253
views
Human Population Reference Genomes (+Neanderthal?)
comparative
genomics
14 hours ago by
emm008
• 0
0
votes
1
reply
171
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
1
reply
168
views
Circos plot using vcf : Mutect2 MultiSample VCF out file
Mutect2
vcf
file
multisample
updated 23 hours ago by
Pierre Lindenbaum
153k • written 1 day ago by
m. bioinfo
• 0
0
votes
2
replies
181
views
Nextflow Stringtie: command not found Error
nextflow
rna-seq
stringtie
updated 30 minutes ago by
ATpoint
70k • written 1 day ago by
selenaajohn
• 0
0
votes
0
replies
194
views
Simes method
simes
method
SNP
R
6 hours ago by
Eliza
▴ 10
5
votes
6
replies
397
views
Nextflow: No space left on device, process using output directory as input?
nextflow
updated 1 hour ago by
Maxime Garcia
▴ 220 • written 2 days ago by
Eliveri
▴ 320
2
votes
4
replies
443
views
msigdbr returns the same genesets for mouse as in for human,
msigdbr
13 hours ago by
e.r.zakiev
▴ 30
4
votes
7
replies
497
views
Calculate RPKM
RPKM
11 hours ago by
Chris
▴ 70
0
votes
5
replies
317
views
install seurat 4.0.3
Seurat
23 hours ago by
Andy
▴ 30
5
votes
3
replies
334
views
News:
March 13-16: Virtual Nextflow and nf-core training event in 5 languages
nf-core
pipeline
Nextflow
updated 3 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 37 minutes 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
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
Criteria for filtering contigs after spades assembly
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Recent Replies
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.
Comment: split fasta file to train deep learning model
by
shenwei356
7.9k
shuffle the sequences, with a rand seed 1. seqkit shuffle --two-pass --rand-seed 1 hairpin.fa -o hairpin.s1.fa testing data …
Comment: split fasta file to train deep learning model
by
pinheirofabiano
▴ 10
I'm trying to split my file in two, using Seqkit, but it is not working.. using the command sample, I can generate a file that contains 80%…
Comment: split fasta file to train deep learning model
by
pinheirofabiano
▴ 10
thank you very much for your comment, @Mensur My file is just a list of peptides, not a complete genome
Comment: March 13-16: Virtual Nextflow and nf-core training event in 5 languages
by
Maxime Garcia
▴ 220
All the videos are now online and organized in 5 different playlists on the nf-core youtube channel: https://www.youtube.com/@nf-core/playl…
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