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1,000 results • Page 1 of 20
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0
votes
0
replies
6
views
TSV with multi-allelic sites to VCF
bcftools
11 minutes ago by Christian ▴ 20
1
vote
1
reply
121
views
Adding MBC/UMI RX tag to read name
umi
15 minutes ago by Christian ▴ 20
0
votes
0
replies
16
views
Spearman correlation rna-seq gene to blood values
spearman rna-seq
updated 34 minutes ago by • 0 • written 37 minutes ago by • 0
0
votes
3
replies
35
views
Java -xmx option does not limit memory usage in the ImputePipelinePlugin?
PHG phg
just now by twrl8 • 0
1
vote
2
replies
26
views
Job: Seeking Jr. Bioinformatician Position
bioinformatician jobsearch
42 minutes ago by santos48 ▴ 40
0
votes
0
replies
9
views
Outgroup for plastome NJ-tree (from pseudoalignment based on SNPs)
bwa-mem2 samtools freebayes mega vcf2phylip
50 minutes ago by poecile.pal ▴ 50
0
votes
0
replies
13
views
Geom bar postive and negative values in a flipped plot
flip_coord ggplot geom_bar
59 minutes ago by luzglongoria ▴ 40
0
votes
2
replies
18
views
getting coding exon information from Ensembl API
API Esembl
30 minutes ago by Sarah ▴ 30
0
votes
0
replies
35
views
displaying results of different RNA-seq projects in R shiny
RNA-seq shiny R
2 hours ago by rls_08 ▴ 40
1
vote
1
reply
42
views
RNAseq: same reads + more complete scaffold = fewer DEGs?
RNAseq
updated 1 hour ago by 4.2k • written 2 hours ago by ▴ 10
729
votes
161
replies
108k
views
100 follow
News: The Biostar Handbook. A bioinformatics e-book for beginners.
training handbook
updated 7 days ago by 1.6k • written 6.3 years ago by 97k
4
votes
7
replies
271
views
GATK GenotypeGVCFs explain
calling gatk variant GenotypeGVCFs
2 hours ago by Sarah ▴ 30
0
votes
0
replies
32
views
calc IBS with vcf files
IBS PLINK
2 hours ago by Mali • 0
0
votes
0
replies
40
views
Hi-C aggregation plot | ARA | PE-Scan
Hi-C
3 hours ago by Argonaut • 0
1
vote
3
replies
54
views
Is it ok to trim assembled paired-end fastq files with cutadapt 3.4 ?
QC cutadapt Illumina trimming 3.4
updated 20 minutes ago by 127k • written 3 hours ago by • 0
1
vote
2
replies
69
views
What is exactly meant by "GENCODE TSS"?
GENCODE transcription annotation TSS gene
updated 1 hour ago by ▴ 50 • written 3 hours ago by ▴ 10
3
votes
2
replies
168
views
Recommendation for (Alternative) Splicing analysis packages for bulk RNA-seq data
splicing RNA-seq
updated 4 hours ago by 3.5k • written 14 hours ago by ▴ 50
0
votes
0
replies
46
views
Job: PhD opportunity in Computer Science / Systems Biology, university of Lille (France)
biology modeling systems job
4 hours ago by cedric.lh • 0
0
votes
1
reply
418
views
SnpSift to annotate vcf with multiple databases
annotate vcf SnpSift
updated 4 hours ago by ▴ 50 • written 15 months ago by ▴ 50
0
votes
1
reply
63
views
SRA Taxonomy Analysis - difference between tables and web
athena taxonomy sra cloud
updated 1 hour ago by 127k • written 5 hours ago by • 0
0
votes
1
reply
90
views
API REST ALINGMENT
api alignment rest python
updated 5 hours ago by ★ 1.0k • written 6 hours ago by ▴ 110
1
vote
2
replies
1.5k
views
Why parametric linkage analysis on Merlin gives zero "0" LOD score?
SNP software error
updated 6 hours ago by • 0 • written 4.9 years ago by ▴ 20
4
votes
3
replies
320
views
How to implement this two-stage one-to-many workflow using WDL?
wdl
updated 7 hours ago by • 0 • written 1 day ago by ▴ 70
0
votes
0
replies
81
views
Does it possible to know what are the adjacent genes up to 1000bp upstream and downstream of IS element
Transposons
7 hours ago by Neel ▴ 10
0
votes
2
replies
711
views
activity of unloaded/unassembled Tn5
sequencing next-gen
updated 6 hours ago by • 0 • written 5.1 years ago by • 0
3
votes
2
replies
138
views
Problem generating a .vcf after upgrade of samtools and bcftools
vcf bam samtools bcftools
10 hours ago by Andy • 0
0
votes
0
replies
71
views
inquiry related to Hi-C data download
Hi-C datasets human brain-cortex interaction matrix
12 hours ago by rheab1230 ▴ 140
0
votes
3
replies
152
views
My fastq files(paired end) have different read number
fastq mapping
updated 5 hours ago by 4.5k • written 13 hours ago by • 0
0
votes
2
replies
144
views
Can I use abundance from Tximport to compare the expression level of transcript in same condition?
Salmon Tximport
updated 13 hours ago by ▴ 50 • written 17 hours ago by ▴ 20
2
votes
4
replies
194
views
Fastqc report analysis
fastqc Fastqc report help trim_galore
12 hours ago by npavliukovec • 0
0
votes
2
replies
143
views
Creating loop for read groups using Picard
bash picard loop
updated 11 hours ago by ▴ 50 • written 15 hours ago by • 0
0
votes
1
reply
108
views
ClusterProfiler enrichKEGG – remove organism name in plots?
KEGG ggplot2 enrichKEGG ClusterProfiler
updated 14 hours ago by ★ 23k • written 15 hours ago by • 0
2
votes
4
replies
2.6k
views
Need help teasing out insertions and deletions with bcftools stats file.vcf > file.stats
bcftools indel vcf insertion deletion
updated 15 hours ago by • 0 • written 5.0 years ago by ▴ 190
0
votes
2
replies
145
views
known-sites for Felis_catus_9.0 (GCA_000181335.4)
Felis-catus GATK
17 hours ago by makarov • 0
3
votes
4
replies
196
views
Creating sample groups from a combination of genes for survival analysis
Survival
4 hours ago by krushnach80 ★ 1.1k
4
votes
5
replies
260
views
RNA-SEQ
NGS RNA-SEQ
8 hours ago by ali • 0
1
vote
4
replies
194
views
Creating a loop to mark duplicates using Picard
bash picard
updated 17 hours ago by 38k • written 19 hours ago by • 0
2
votes
3
replies
150
views
Active enhancers for mm39
bed coordinates enhancers mm39
updated 10 hours ago by 11k • written 20 hours ago by ▴ 690
0
votes
0
replies
82
views
News: course - Reproducibility in Bioinformatics
Bioinformatics Docker Reproducibility
19 hours ago by carlopecoraro2 ★ 2.3k
0
votes
4
replies
181
views
Mapping paired end reads with ngm and samtools, using prefixes and suffixes for creating vcf eventually
ngm sam samtools
4 hours ago by Human • 0
3
votes
2
replies
137
views
Power analysis for patient samples
RNA-seq
19 hours ago by aropri ▴ 130
0
votes
4
replies
314
views
Circos plot using vcf : Mutect2 MultiSample VCF out file
Mutect2 vcf
1 hour ago by m. bioinfo • 0
0
votes
2
replies
124
views
OrthoFinder problem
Sub OrthoFinder iterative processes Bash
2 hours ago by HERMAN ▴ 10
4
votes
2
replies
146
views
Forum: advice on course selection for a bioinformatics career.
career
updated 21 hours ago by 97k • written 21 hours ago by • 0
0
votes
1
reply
109
views
Error when using compareCluster from enichment
compareCluster
updated 5 hours ago by ★ 1.4k • written 21 hours ago by • 0
0
votes
0
replies
88
views
Need Help Scraping MeSH terms from Pubmed
Python Entrez Scraping
updated 21 hours ago by 38k • written 22 hours ago by • 0
1
vote
1
reply
108
views
NA14622 data for benchmarking
benchmarking vcf bed GiAB
updated 21 hours ago by 127k • written 22 hours ago by ▴ 110
0
votes
2
replies
147
views
How to add gene information below the BSmooth result ?
BSmooth methylation DNA
16 hours ago by diqixiaoyaoer ▴ 10
1
vote
1
reply
127
views
Plot in R: Presence of bacteria type A vs bacteria type B in different groups
boxplot phyloseq plot abundance ggplot2 R
updated 22 hours ago by ★ 1.4k • written 22 hours ago by • 0
2
votes
1
reply
96
views
Fastqc lsequence duplication and per base sequence content failed
RNA-seq fastqc
updated 22 hours ago by 127k • written 23 hours ago by ▴ 150
1,000 results • Page 1 of 20
Recent Votes
Recommendation for (Alternative) Splicing analysis packages for bulk RNA-seq data
Answer: Adding MBC/UMI RX tag to read name
Comment: Is it ok to trim assembled paired-end fastq files with cutadapt 3.4 ?
Transforming And Manipulating Color Space Reads
Comment: Seeking Jr. Bioinformatician Position
Comment: 10x 3' library creates R1 and R2 fastq files with the same read length
The Biostar Handbook. A bioinformatics e-book for beginners.
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Scholar to Trivas ▴ 660
Scholar to Christian ▴ 20
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Recent Replies
Answer: Adding MBC/UMI RX tag to read name by Christian ▴ 20
# this script takes a BAM file and moves the UMI tag from the RX tag # and appends it to the read name # argument 1: input fi…
Comment: Is it ok to trim assembled paired-end fastq files with cutadapt 3.4 ? by GenoMax 127k
> I´m concatenating two sets of files before trimming to remove > sequences from both of them That only makes sense if it is the same samp…
Comment: getting coding exon information from Ensembl API by Sarah ▴ 30
Why does this bother you ! Who is you ? the admin of this forum ? we are here to learn, not to be watched. Dont comment my post again ple…
Comment: Is it ok to trim assembled paired-end fastq files with cutadapt 3.4 ? by Bengisu • 0
Thank you for sharing. I´m concatenating two sets of files before trimming to remove sequences from both of them. But, I don´t know if it i…
Comment: getting coding exon information from Ensembl API by Pierre Lindenbaum 153k
[again, and again and again, so many questions and no validation][1] [1]: https://www.biostars.org/u/67462?active=posts
Comment: Seeking Jr. Bioinformatician Position by santos48 ▴ 40
Thank you so much, I will also add my e-mail.
Comment: Seeking Jr. Bioinformatician Position by GenoMax 127k
There is no way for people to contact you (via personal messages or otherwise) on this forum. You may want to look at alternate avenues if …
Comment: Snakemake vs Nextflow Upcoming bioinformatics Project by colindaven 4.5k
Don't worry about groovy too much. I have been writing productive nextflow pipelines for a couple of years and still haven't learned much i…
Comment: Java -xmx option does not limit memory usage in the ImputePipelinePlugin? by lcj34 ▴ 220
Does the amount of memory keep increasing, or does it start high and remain stable? Do you have a log file you can post? That may give us…
Comment: 10x 3' library creates R1 and R2 fastq files with the same read length by GenoMax 127k
> Then, we can just effectively ignore everything from bp 29 onwards? Yes.
Comment: 10x 3' library creates R1 and R2 fastq files with the same read length by bompipi95 ▴ 120
Hi! Jusrt so that I understand this correctly, for the 10x v3 libraries sequenced on Novaseq, does it mean that if R1 is 150bp and looks li…
Comment: Java -xmx option does not limit memory usage in the ImputePipelinePlugin? by GenoMax 127k
Based on the program name `run_pipeline.pl` this appears to be a perl script. Option you are referring to is for `Java`. Is that perl scrip…
Comment: Is it ok to trim assembled paired-end fastq files with cutadapt 3.4 ? by GenoMax 127k
> So, I prefer to work assembled fastq files into one fastq rather than > two. What does this mean? Are you concatenating two sets of file…
Comment: What is exactly meant by "GENCODE TSS"? by ntsopoul ▴ 50
checkout: chipseeker package there is a function which gets you the tss getPromoters(TxDb=txdb, upstream=3000, downstream=3000) as you c…
Comment: SRA Taxonomy Analysis - difference between tables and web by GenoMax 127k
> Apparently it is ok for some accessions In that case, your best bet is to contact NCBI help desk with examples of what works and what do…
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