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697 results • Page 2 of 14
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4
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3
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191
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when I use htslib to write a bam. Error of "truncated file" shows by samtools
bam htslib
updated 10 minutes ago by 142k • written 17 hours ago by ▴ 10
4
votes
6
replies
12k
views
Looking for differential gene expression between treatment, within a specific cluster (seurat)
seurat
updated 2 days ago by ★ 17k • written 4.7 years ago by ▴ 230
4
votes
7
replies
472
views
How does gene length effect the number of reads mapped
RNA-seq CPM sequencing
15 days ago by Chen • 0
4
votes
6
replies
441
views
Mouse or Rat Gene Expression Data Similar to GTEx
whole-body expression atlas
5 days ago by Shicheng Guo ★ 9.4k
4
votes
2
replies
306
views
GRCh38.gmap file
gnomix gmap
24 days ago by lorena9132 ▴ 10
4
votes
4
replies
3.0k
views
CNVkit for somatic copy number detection
cnv cnvkit exome WES
updated 15 days ago by ▴ 10 • written 5.1 years ago by • 0
4
votes
12
replies
4.9k
views
10 follow
How to analyze Infinium Mouse Methylation BeadChip array data?
Methylation Experience Illumina Mouse
updated 19 days ago by ▴ 180 • written 3.1 years ago by ▴ 20
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 20 days ago by ▴ 10 • written 2.6 years ago by • 0
4
votes
9
replies
678
views
In one PCA plot, can I calculate the percentage of different factors that contribute to the PCA?
PCA R VARIANCE
updated 8 days ago by ▴ 140 • written 13 days ago by ▴ 20
4
votes
1
reply
244
views
PCA plot no distinct cluster. Only p < 0.05 indicates significant DEGs, while adj p < 0.05 does not.
RNA-seq padj p-value
updated 5 days ago by 14k • written 5 days ago by • 0
4
votes
12
replies
903
views
6 follow
DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts in whole blood: is it normal to always get NS?
rstudio DEG limma
updated 6 hours ago by ★ 7.2k • written 14 days ago by • 0
4
votes
9
replies
2.2k
views
6 follow
Same sequencing sample in multiple lanes. How to analyse it?
sequencing bowtie2 alignment samtools ngs
updated 25 days ago by • 0 • written 2.2 years ago by • 0
4
votes
3
replies
437
views
Kraken2 database
kraken microbialdb database krakendb kraken2
updated 15 days ago by ▴ 150 • written 18 days ago by ▴ 10
4
votes
1
reply
364
views
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
limma
updated 14 days ago by 14k • written 15 days ago by ▴ 30
4
votes
6
replies
3.9k
views
How to interpret DEXseq results in therms of significance
DEXseq RNA-Seq exon
updated 22 days ago by ▴ 30 • written 6.7 years ago by ★ 1.3k
4
votes
6
replies
349
views
Error with BiocParallel. No barcodes files found
Barcodes scRNA-seq SingleCellExperiment
5 days ago by bio_info ▴ 20
4
votes
1
reply
236
views
Extracting only 4-fold degenerate sites from gene sequences/alignments?
alignments
14 days ago by J. ▴ 40
4
votes
1
reply
282
views
LD-prune variants while maintaining a list of SNPs
snp vcf plink filtering independent
updated 23 days ago by 11k • written 24 days ago by ▴ 570
4
votes
2
replies
253
views
Number of non-ATCG nucleotides replaced by Salmon
rna-seq stringtie salmon
updated 1 day ago by 44k • written 4 days ago by ▴ 10
4
votes
3
replies
3.0k
views
How to solve the error 'ERROR::MATE_NOT_FOUND:Found xxx unpaired mates' when run SamToFastq
samtofasq picard validatesamfile
updated 20 days ago by 162k • written 20 days ago by ★ 1.3k
4
votes
5
replies
3.5k
views
How to compare compare two Sam files to check mapping
alignment
updated 20 days ago by ▴ 90 • written 6.5 years ago by ▴ 60
4
votes
1
reply
378
views
How to use limma to find differentially expressed genes in response to a continuous variable
limma voom R
29 days ago by pairedttest ▴ 10
4
votes
9
replies
558
views
Faster Needleman-Wunsch rapid global alignment of two sequences?
Needleman-Wunsch alignment
11 days ago by Gabriel R. ★ 2.9k
4
votes
6
replies
3.9k
views
Taking the difference of two VCFs (or removing singletons)
genome sequencing singleton SNP filter
updated 29 days ago by ▴ 20 • written 9.7 years ago by ▴ 40
4
votes
0
replies
176
views
Herald: The Biostar Herald for Monday, April 29, 2024
herald
29 days ago by Biostar 2.8k
4
votes
15
replies
1.7k
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 25 days ago by ★ 7.2k • written 5 months ago by ▴ 10
4
votes
9
replies
2.1k
views
Legend and hap files for imputation with 38 build
reference 38build impute imputation
29 days ago by anna ▴ 20
4
votes
2
replies
219
views
Duplicated sequence samtools
bowtie2 samtools
updated 15 days ago by 142k • written 15 days ago by • 0
3
votes
5
replies
280
views
Invalid CIGAR after using bam clipOverlap
validatesamfile cigar bam clipoverlap
7 hours ago by MboiTui ▴ 20
3
votes
8
replies
6.7k
views
7 follow
GATK genomicsDBimport intervals for WGS
gatk genomicsdbimport
updated 26 days ago by • 0 • written 5.2 years ago by 11k
3
votes
4
replies
4.1k
views
FarmCPU - how to explain the reported 'effect'?
gwas
updated 20 days ago by • 0 • written 5.6 years ago by 8.5k
3
votes
6
replies
561
views
install package: package ‘gmwm’ is not available for this version of R
r
updated 16 days ago by ▴ 20 • written 23 days ago by • 0
3
votes
0
replies
131
views
Comparing ATAC-seq narrowPeak Files from Chicken and Mouse
liftOver ATAC-seq csaw
updated 7 days ago by 44k • written 7 days ago by ★ 1.2k
3
votes
8
replies
888
views
Random Access remote BAM files
htslib BAM
updated 6 days ago by • 0 • written 3 months ago by ▴ 20
3
votes
4
replies
212
views
How do i calculate the mean of triplicates in a data.frame based on pattern?
tidyverse r
updated 44 minutes ago by 14k • written 1 day ago by ★ 1.9k
3
votes
2
replies
187
views
How to interpret this plotMDS of three disease clusters?
microarray plotMDS DEGs
updated 5 days ago by 82k • written 6 days ago by • 0
3
votes
12
replies
5.4k
views
7 follow
txt file to bigwig
MEME bigwig
updated 20 hours ago by 142k • written 8.6 years ago by ▴ 50
3
votes
2
replies
213
views
vg autoindex seems stuck after a week of running
vg pangenome
1 day ago by StevieP ▴ 10
3
votes
8
replies
775
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 22 days ago by ▴ 410 • written 26 days ago by ▴ 100
3
votes
3
replies
405
views
What analysis suitable to identify similarly expressed genes between two samples (treated vs untreated). Contrary to DGE analysis,
Gene-Expression RNA NOISeq DGE
updated 26 days ago by 82k • written 26 days ago by • 0
3
votes
9
replies
1.6k
views
Rseqc infer_experiment.py: 0 usable reads sampled and unknown data type
rseqc infer_experiment.py RNA-seq
updated 10 hours ago by • 0 • written 17 months ago by ▴ 40
3
votes
3
replies
310
views
what is another word for a BLAST "hit"?
blast alignment
18 days ago by dec986 ▴ 380
3
votes
3
replies
477
views
absolute path for symbolic links in Snakefile
Snakemake
updated 19 days ago by ▴ 770 • written 5 weeks ago by ▴ 60
3
votes
4
replies
360
views
Getting differential ChIP-seq peaks between conditions after calling consensus peaks
MAnorm ChIP-seq consensus peaks
2 days ago by Alexandra • 0
3
votes
3
replies
320
views
Gene Specific coverage from WGS data
WGS SARS-CoV2
updated 15 days ago by 44k • written 29 days ago by • 0
3
votes
2
replies
232
views
Publish a Letter in higher impact vs Research article in lower impact
Article Letter Journal
updated 16 days ago by 82k • written 16 days ago by • 0
3
votes
4
replies
515
views
Design matrix Differential expression analysis
RNA-seq Differential-expression
updated 22 days ago by ★ 7.2k • written 25 days ago by ▴ 40
3
votes
5
replies
489
views
Practical Haplotype Graph v2 not finding correct paths
Pangenome PHG graph
7 days ago by beantkapoor16 ▴ 10
3
votes
2
replies
451
views
Extract protein sequence
fasta alignment blast
28 days ago by anna ▴ 20
3
votes
2
replies
300
views
imputation through beagle
panel beagle reference imputation
15 days ago by analyst ▴ 50
697 results • Page 2 of 14
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Comment: bcl-convert cannot create output directory structure at the path specified
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Recent Replies
Comment: when I use htslib to write a bam. Error of "truncated file" shows by samtools by GenoMax 142k
https://www.biostars.org/u/110878/ : Please accept this answer (green check mark) to provide closure to this thread.
Comment: bcl-convert cannot create output directory structure at the path specified by giulia.trauzzi ▴ 10
Thanks! I am sure there are. Are these necessary to demultiplex the data though? I am assuming most demultiplexing tools do not require the…
Comment: Filtering reads that map to both references by GenoMax 142k
You can use `bbsplit.sh` from BBMap suite to map reads to multiple references and bin them accordingly. Take a look at the in-line help (`a…
Comment: bcl-convert cannot create output directory structure at the path specified by GenoMax 142k
Is that the only error? Can you provide the entire command line you are using? > as a customer is interested in getting the fastq files f…
Comment: Filtering reads that map to both references by michael.flower.14 ▴ 180
Thanks Pierre. I'm working in a micromamba environment. I've got `jvarkit` installed. I updated your filter script as follows. # Creat…
Comment: bcl-convert cannot create output directory structure at the path specified by giulia.trauzzi ▴ 10
Hi, thanks for this. I checked the permissions of the folder and changed them with chmod ugo+rwx /output_directory This has changed …
Comment: RNA-Seq analysis by carlopecoraro2 ★ 2.5k
[Online course: ANALYSIS OF RNA SEQUENCING DATA WITH R/BIOCONDUCTOR][1] ---------- Dates 4-15 November 2024 [1]: https://www.physal…
Comment: How do i calculate the mean of triplicates in a data.frame based on pattern? by dariober 14k
I guess the OP doesn't want to hard-code `p767.AM` and `"AM"`?
Comment: bcl-convert cannot create output directory structure at the path specified by marco.barr ▴ 140
I've never received this error before.. but you could try checking the permissions
Answer: How do i calculate the mean of triplicates in a data.frame based on pattern? by gglim ▴ 140
``` library(dplyr) df %>% rowwise() %>% mutate(p767.AM = mean(c_across(contains("AM")))) ``` Maybe this is what you're looking for?
Answer: RNA-Seq analysis by Michael 54k
I think the situation you are finding yourself in is quite common. On a general note, as you are at the beginning of your PhD program, you …
Answer: RNA-Seq analysis by Nat.Nataren ▴ 30
We'll need a lot more information to help, you haven't given us much to work with. What organism are you working in? What is the experi…
Comment: Cut&Run and heatmap by gglim ▴ 140
I'll take a look at these peaks in IGV with the signal files and set a threshold for filtering.
Comment: NCBI vs Ensembl - Ortholog genes Information by José ▴ 10
Thanks for the answer and the advice.
Comment: NCBI vs Ensembl - Ortholog genes Information by José ▴ 10
Thak you so much for your answer and advice.
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