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10
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16
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17k
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7 follow
How Can I Count Snps In My Final Vcf Files
SNP
updated 2 days ago by 161k • written 5.7 years ago by ▴ 180
4
votes
15
replies
1.6k
views
how to test for differential expression in samples where a global increase in gene expression is expected
edgeR DESeq Differential-Expression RNA-Seq
updated 5 days ago by ★ 7.1k • written 4 months ago by ▴ 10
10
votes
14
replies
656
views
6 follow
Bacterial plasmid analysis
bacteria plasmid wgs hybridassembly sequencing
updated 2 days ago by 142k • written 8 days ago by • 0
13
votes
14
replies
803
views
High Malat-1 expression in single cell data
single-cell
updated 1 day ago by ▴ 40 • written 10 days ago by ▴ 40
4
votes
12
replies
4.8k
views
10 follow
How to analyze Infinium Mouse Methylation BeadChip array data?
Methylation Experience Illumina Mouse
updated 7 hours ago by ▴ 180 • written 3.0 years ago by ▴ 20
16
votes
12
replies
7.4k
views
10 follow
how to split multi-fasta file into single fasta file named by header
genome perl python3 bash python
updated 6 days ago by ▴ 10 • written 3.1 years ago by ▴ 120
1
vote
11
replies
5.5k
views
Truncated Bam Error
R next-gen sequencing software error
updated 3 days ago by • 0 • written 6.1 years ago by ▴ 20
2
votes
11
replies
2.6k
views
6 follow
CNVKIT - unable to produce scatter and diagram pdfs
cnvkit
updated 1 day ago by • 0 • written 4.8 years ago by ▴ 60
1
vote
10
replies
857
views
error to run rnammer
phylogenomics rRNA_extraction rnammer
updated 3 days ago by • 0 • written 4 months ago by ▴ 30
0
votes
9
replies
1.5k
views
kinannote software installation problems
kinannote
updated 1 day ago by • 0 • written 5.7 years ago by ▴ 30
4
votes
9
replies
2.1k
views
6 follow
Same sequencing sample in multiple lanes. How to analyse it?
sequencing bowtie2 alignment samtools ngs
updated 6 days ago by • 0 • written 2.2 years ago by • 0
3
votes
8
replies
563
views
Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA2 - where to go from here?
nf-core 16S amplicon dada2 ampliseq
updated 3 days ago by ▴ 410 • written 7 days ago by ▴ 100
3
votes
8
replies
522
views
How to access TCGA samples that were treated with a specific drug?
TCGA RNA-seq
3 days ago by Qroid ▴ 40
0
votes
8
replies
170
views
Different output for read length
samtools BAM
1 hour ago by marco.barr ▴ 100
1
vote
7
replies
458
views
Downsampling long-read BAM files
nanopore BAM QC ONT downsampling
6 days ago by eebloom ▴ 80
0
votes
7
replies
445
views
Applying the metacell2 algorithm using python
python single-cell scanpy metacell2
updated 1 day ago by ★ 2.0k • written 3 days ago by ▴ 140
1
vote
7
replies
474
views
Question regarding WGCNA
WGCNA Network-construction
7 hours ago by deepak • 0
0
votes
7
replies
575
views
Post-imputation plot
michigan-imputation-server quality-control
updated 6 days ago by 3.9k • written 10 days ago by ▴ 10
0
votes
6
replies
426
views
Differential Expression Analysis using DESeq2 in R
deseq2 R
updated 6 days ago by 14k • written 6 days ago by • 0
0
votes
6
replies
2.1k
views
Copy number Variation analysis using conumee
R software error sequencing genome
updated 10 hours ago by 142k • written 3.2 years ago by ▴ 10
1
vote
6
replies
359
views
Do I need to go back and filter my long-reads?
alignment nanopore filtering QC ONT
updated 6 days ago by 142k • written 24 days ago by ▴ 80
0
votes
6
replies
315
views
How does gene length effect the number of reads mapped
RNA-seq CPM sequencing
updated 6 days ago by ★ 6.0k • written 7 days ago by • 0
1
vote
6
replies
685
views
anRichment is missing
WGCNA anRichment
updated 3 days ago by 142k • written 5 months ago by ▴ 180
6
votes
6
replies
1.8k
views
agilent human all exon sureselct v7 bed file
exon human bed v7 agilent all sureselect
updated 4 days ago by ▴ 10 • written 24 months ago by • 0
4
votes
6
replies
3.8k
views
How to interpret DEXseq results in therms of significance
DEXseq RNA-Seq exon
updated 3 days ago by ▴ 30 • written 6.7 years ago by ★ 1.2k
4
votes
6
replies
1.2k
views
Soft-clipping read ends based on read group
ancient molecule at bam DNA RG ends clipping damage
updated 1 day ago by ▴ 10 • written 2.5 years ago by • 0
5
votes
5
replies
620
views
Tutorial: how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix RNAseq R
updated 6 days ago by • 0 • written 14 days ago by ★ 3.9k
0
votes
5
replies
328
views
RNAseq one control two conditions, shared and exclusive genes
conditions RNAseq multiple Rstudio
updated 6 days ago by ▴ 20 • written 10 days ago by • 0
3
votes
5
replies
340
views
Converting CRAM to FastQ
GATK samtools cram SamToFastq fastq
6 days ago by Maverick ▴ 10
1
vote
5
replies
310
views
Comparative Analysis of Algorithms for Implementing the FM-Index: Correctness, Complexity, and Use Cases
fmindex bwt
updated 1 day ago by 54k • written 2 days ago by • 0
5
votes
5
replies
263
views
Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent
EGSEA
1 day ago by Chris ▴ 280
1
vote
5
replies
345
views
Introduce SNPs on FASTA
simulation snps haplotypes pharmacogenetics
6 days ago by Riccardo ▴ 10
1
vote
5
replies
203
views
UMI-Tools knee-method has great influence on the results of white list
single-cell whitelist UMI RNA UMI-Tools
updated 2 days ago by 19k • written 2 days ago by ★ 1.8k
2
votes
5
replies
2.5k
views
identifying transgene insertion site in WGS
WGS insertion site trangene de-novo soap
updated 1 day ago by • 0 • written 5.1 years ago by ★ 1.8k
0
votes
5
replies
265
views
A question about reference genome for creating the consensus sequence
fasta fa cram genome
1 day ago by me • 0
1
vote
5
replies
306
views
install.packages("imudata") - package ‘imudata’ is not available for this version of R
r
updated 3 days ago by 43k • written 3 days ago by • 0
0
votes
5
replies
371
views
6 follow
What purposes can TPM values be used for?
RNA-seq TPM Normalization DESeq2
updated 6 days ago by ▴ 180 • written 7 days ago by • 0
0
votes
5
replies
221
views
Percentage coverage of reference genome by de novo genome
SAMtools BWA alignment ddRAD
updated 1 day ago by 21k • written 1 day ago by • 0
3
votes
5
replies
288
views
Generating mpileup file using samtools
mpileup samtools
updated 6 days ago by 21k • written 6 days ago by • 0
1
vote
5
replies
376
views
install package: package ‘gmwm’ is not available for this version of R
r
updated 3 days ago by 43k • written 4 days ago by • 0
4
votes
5
replies
3.4k
views
How to compare compare two Sam files to check mapping
alignment
updated 1 day ago by ▴ 90 • written 6.4 years ago by ▴ 60
1
vote
5
replies
399
views
HCL database download
HCL
updated 1 day ago by 43k • written 5 days ago by ▴ 20
0
votes
5
replies
353
views
Easy way to find out which allele is minor allele from bed file?
plink
updated 5 days ago by 10k • written 6 days ago by ▴ 750
0
votes
5
replies
340
views
Filtering Multi-sample VCF file for all except one Genotype
variant SNP VCF
updated 5 hours ago by 22k • written 2 days ago by • 0
1
vote
4
replies
179
views
Importing a fastq file
Fastq
14 hours ago by oumo • 0
0
votes
4
replies
380
views
Highest variable features in single cell data
single-cell
2 days ago by carolofharvest ▴ 40
1
vote
4
replies
362
views
Segmentation error while using a tool
smalt
updated 5 days ago by ★ 27k • written 5 days ago by • 0
2
votes
4
replies
710
views
Count all variants from vcf file
variants vcf Count
updated 2 days ago by 161k • written 20 months ago by • 0
1
vote
4
replies
348
views
Understanding STAR output (Aligned.out.sam file)
STAR paired-end read
2 days ago by heelpPlease • 0
3
votes
4
replies
417
views
Design matrix Differential expression analysis
RNA-seq Differential-expression
updated 2 days ago by ★ 7.1k • written 5 days ago by ▴ 40
194 results • Page 1 of 4
Recent Votes
Deeptools computematrix of scale region give different result from ref point TSS.
course on Landscape Genomics at the EPFL in Lausanne (June 17-21)
course on Landscape Genomics at the EPFL in Lausanne (June 17-21)
cellranger error message
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA
Network plot from expression data in R using igraph
Comment: RNA seq analysis
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Recent Replies
Comment: Truncated metadata file report from ENA Portal API by GenoMax 142k
Are you missing a `"` at the end of the URL. Doing wget -O test.out "https://www.ebi.ac.uk/ena/portal/api/filereport?accession=PRJNA43…
Comment: Different output for read length by marco.barr ▴ 100
very strange, I double checked the BAM file and it is the same one I used for your request. Are the commands I wrote above correct? How is …
Comment: Different output for read length by Pierre Lindenbaum 161k
the first read as a length of 1747, i wonder how you can just find '50' $ wget -qO - "https://gist.githubusercontent.com/Macdot3/4650…
Comment: Problem with Seurat package in PercentageFeatureSet function by bk11 ★ 2.4k
Yes, `CreateAssayObject` function is used for only expression matrix.
Comment: Different output for read length by marco.barr ▴ 100
Here is my result, I hope you can see it. [https://gist.github.com/Macdot3/4650243a10540d8c06f728ffc16a136c][1] [1]: https://gist.gith…
Comment: Different output for read length by marco.barr ▴ 100
I just published my link on paste, why can't I see my public paste on the site?
Comment: cellranger error message by Max • 0
I'm having a similar issue. The sample_id matches the filename prefix before _S1_L001, but I get the error: Log message: Requested sample(s…
Comment: Different output for read length by marco.barr ▴ 100
Thanks so much GenoMax, I'm sharing the link as you told me
Comment: Different output for read length by GenoMax 142k
Post the data at pastebin.com and add a link here or you could a GitHub gist. You were suspended by biostars SPAM bot since you pasted link…
Comment: Different output for read length by GenoMax 142k
Post the data at pastebin.com and add the link here. You were suspended by biostars SPAM bot since you pasted these links in quick successi…
Comment: RNA seq analysis by s.ghazala • 0
Could you clarify on what exactly you are referring to with "SRA data table". If you are retrieving fastq files (raw data), then you could …
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA by sovrappensiero ▴ 100
Thanks, Chris. I really appreciate your help. This has clarified a lot for me!
Answer: Snakemake fails to find conda in PBS by tim.booth ▴ 50
Snakemake does not have support for micromamba. There is an open issue: https://github.com/snakemake/snakemake/issues/2322
Comment: absolute path for symbolic links in Snakefile by tim.booth ▴ 50
Further to this answer - if you are using GNU coreutils (ie. any modern Linux), there is a "-r" flag to fix this problem. I typically use "…
Answer: Different output for read length by Pierre Lindenbaum 161k
I supect your reads are hard clipped. Show us the first lines of samtools view /home/sorted.bam | cut -f 2,6,10 | head -n 20
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