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0
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7
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4.2k
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align_and_estimate_abundance.pl (rsem-parse-alignments: /lib64/libz.so.1: version `ZLIB_1.2.3.3' not found (required by rsem-parse-alignments))
RNA-Seq alignment software-error next-gen sequence
updated 5 days ago by 41k • written 5.6 years ago by • 0
1
vote
3
replies
2.2k
views
BBMap : NH:i:1 and XT:A:R
bbmap
updated 19 days ago by ▴ 10 • written 7.1 years ago by 10k
2
votes
6
replies
2.1k
views
No best K value found
Assembly Kmergenie
updated 17 days ago by • 0 • written 6.8 years ago by ▴ 80
0
votes
7
replies
1.6k
views
CIBERSORTx error: 'x' must be an array of at least two dimensions
matrix CIBERSORTx signature
updated 24 days ago by • 0 • written 17 months ago by • 0
1
vote
5
replies
1.5k
views
BLAST: overflow error
BLAST
updated 7 days ago by 136k • written 19 months ago by ▴ 60
0
votes
2
replies
1.5k
views
Does GNOMAD use all LOFTEE LoF filters?
loftee gnomad LOF ensembl vep
updated 9 days ago by • 0 • written 3.8 years ago by ▴ 50
0
votes
2
replies
1.5k
views
AttributeError: module 'collections' has no attribute 'Hashable'
Spades
updated 12 days ago by ▴ 20 • written 7 months ago by ▴ 30
1
vote
1
reply
1.3k
views
How to interpret the discrepancy of assignment rate in featurecounts using forward and reverse strand protocols
RNAseq
updated 5 days ago by • 0 • written 7 weeks ago by ▴ 20
0
votes
7
replies
1.2k
views
Comparing the GVF file & VCF file
gvf dna vcf ensembl ngs
updated 24 days ago by • 0 • written 10 months ago by ▴ 30
0
votes
4
replies
1.2k
views
Adding functional annotation and meta-data of MAKER/BRAKER GFF
metadata functional-annotation BRAKER MAKER
updated 10 days ago by ▴ 10 • written 11 months ago by ▴ 20
0
votes
1
reply
1.1k
views
GATK4 -known-sites input Recalibrate Base Quality Scores
Plant GATK NGS Variant-Calling
updated 28 days ago by 41k • written 2.1 years ago by • 0
0
votes
1
reply
1.1k
views
How to interpret Nucleosome banding pattern in scATAC-Seq?
single-cell scATAC-Seq Signac transcriptomics
updated 20 days ago by ★ 2.7k • written 2.1 years ago by ▴ 290
0
votes
3
replies
1.0k
views
Error with Ice normalization when running HiC-Pro
Hi-C HiChIP HiC-Pro
updated 6 days ago by 41k • written 2.1 years ago by • 0
0
votes
1
reply
985
views
How to run Aracne cytoscape plugin ?
R software error rna-seq
updated 2 days ago by • 0 • written 3.2 years ago by ▴ 50
0
votes
0
replies
891
views
Any tools for finding the telomere sequences / lengths directly for nanopore sequencing reads without any prior knowledge of the organism
genomics telomeres reads
17 days ago by Mark • 0
0
votes
0
replies
878
views
For people doing high molecular weight DNA sequencing library prep, do you see a steep drop off in the fragment sizes before and after the library pr…
library-prep sequencing ont nanopore ngs
19 days ago by Mark • 0
9
votes
15
replies
876
views
Construction of single sequence assembly out of contigs
Contigs Bacteria Genome WGS
12 days ago by analyst ▴ 10
1
vote
1
reply
866
views
cellphonedb results visualization
cellphonedb ktplotspy cpdb visulization
updated 19 days ago by ▴ 20 • written 10 months ago by ▴ 20
2
votes
2
replies
841
views
Using ggplot2 to make barplots of RNASeq data - maintaining sample metadata when pivoting from wide to long format
rnaseq pivot_longer ggplot2
updated 12 days ago by ★ 3.5k • written 12 days ago by • 0
0
votes
3
replies
817
views
"MethylKit" package for WGBS data
MethylKit WGBS
updated 9 days ago by • 0 • written 2.4 years ago by ▴ 20
2
votes
5
replies
720
views
Pre-processing for Agilent microarray data?
affymetrix microarray gene agilent rna
updated 24 days ago by ★ 1.1k • written 6 months ago by • 0
2
votes
11
replies
719
views
Data preparation for a ML model
machine-learning RNA-Seq R python biomarkers
11 days ago by sil_bioinfo ▴ 40
2
votes
9
replies
712
views
Salmon (or other pseudo-mappers) for multi-species RNAseq read filtering
STAR Salmon mapper aligner RNAseq
11 days ago by ian.will ▴ 10
0
votes
0
replies
702
views
Generating variant read count matrix, total read count matrix and binary/ternary mutaion matrix for SNV from scDNAseq FASTQ files
SNV mutationMatrix tumorPhylogeny scDNAseq mutaion
4 days ago by supernovamik • 0
0
votes
1
reply
691
views
Alternative tool for split'N'trim
SNP Galaxy Single-cell RNA-seq
updated 5 days ago by 41k • written 3.6 years ago by ▴ 30
0
votes
4
replies
684
views
How to resolve the error of protein lacking a stop codon when using GenomeThreader for homology prediction?
genome threader
5 days ago by peanut • 0
0
votes
1
reply
683
views
Seurat PlotClusterTree together with heatmap of gene expression
seurat heatmap clustering single-cell
updated 21 days ago by 41k • written 7 months ago by ▴ 20
0
votes
2
replies
660
views
Regarding Error query in publically available RNA seq analysis by R studio
GEO Rstudio RNA-seq NGS
updated 5 days ago by 41k • written 2.2 years ago by • 0
0
votes
1
reply
643
views
Trouble with Ligand-Protein Docking in AutoDock Vina: Shows an error when docked against a new set of ligands
Docking Protein-receptor Ligand-Protein-Docking AutoDock-Vina
updated 25 days ago by 41k • written 25 days ago by • 0
0
votes
1
reply
631
views
How to determine E. coli MLST (Multi Locus Sequence Typing ) from the sequencing of the PCR product of 7 housekeeping genes
MLST phylogenetic nanopre
updated 6 days ago by 21k • written 6 days ago by • 0
0
votes
4
replies
619
views
WGCNA Analysis - blockwiseModules data processing
WGCNA blockwiseModules
updated 24 days ago by 136k • written 3 months ago by ▴ 90
0
votes
3
replies
619
views
Gene family classification using RNA-seq data
gene-expression RNA-seq gene-family
updated 5 days ago by 41k • written 8 months ago by • 0
2
votes
2
replies
609
views
6 follow
Why runing scDblFinder before and after removing low QC cells gives different results
singleCellExperiment scDblFinder SMART-Seq
updated 14 days ago by ▴ 170 • written 5 months ago by ★ 1.8k
1
vote
3
replies
603
views
How to find DEG with deseq2 in R
GSE RNA-seq deseq2
updated 5 days ago by 41k • written 13 months ago by • 0
1
vote
8
replies
595
views
Mitochondrial genes - TPM calculation bulk RNA-Seq
TPM RNA-Seq mtDNA
25 days ago by nick_b55 ▴ 10
3
votes
7
replies
589
views
IGV not showing bigwig track information
bigwig IGV ChIP-seq
updated 27 days ago by 78k • written 4 weeks ago by ▴ 10
4
votes
7
replies
577
views
SNP IDs
SNP
26 days ago by kl ▴ 10
0
votes
6
replies
573
views
Add braces to the DNA sequence for re quested primer position.
python subprocess
updated 26 days ago by 41k • written 4 weeks ago by • 0
0
votes
7
replies
562
views
Issue with Merging BCF Files: Invalid INFO id Error
bcftools
updated 21 days ago by 41k • written 23 days ago by • 0
0
votes
6
replies
557
views
Help locating TCGA data from cbioportal
cancer TCGA RNA cbioportal CNA
26 days ago by ConvolutedGenome ▴ 20
1
vote
6
replies
556
views
Problem aligning target capture sequencing of a few hundred regions to the human reference genome
GATK4 bwa-mem target-capture-sequencing alignment
18 days ago by Miguel • 0
1
vote
1
reply
555
views
fragments.tsv.gz file in ATAC seq
ATAC-seq
updated 14 days ago by ▴ 10 • written 8 months ago by ▴ 230
1
vote
6
replies
535
views
frequency plot for peaks
chip-seq chipseeker
updated 12 days ago by ▴ 400 • written 27 days ago by ▴ 10
1
vote
8
replies
535
views
DESEQ2 design in DESeqDataSetFromMatrix: cell and treatment
rna-seq deseq2
21 days ago by pingu77 ▴ 20
0
votes
2
replies
529
views
Understanding gene level copy number data from TCGAbiolinks
CNV TCGA
updated 7 days ago by ★ 1.1k • written 13 months ago by • 0
0
votes
1
reply
517
views
Problems separating and converting molecule files with openbabel
openbabel
updated 6 days ago by ▴ 50 • written 16 months ago by • 0
0
votes
0
replies
511
views
How I get fraction fragments in peak without metadata in sc ATAC-seq with Signac ?
atac-seq seurat signac single-cell
updated 21 days ago by 41k • written 11 months ago by • 0
0
votes
0
replies
504
views
Transcript Assembly for Multiple Species Using StringTie and Orthogroup Discovery using OrthoFinder
Species StringTie Orthogroups Transcript Assembly
2 days ago by dtnondorf • 0
3
votes
6
replies
498
views
scRNA-seq: Consistent low number of cells and low fraction reads across the samples
scRNA-seq cells mRNA expression gene
updated 10 days ago by ★ 1.3k • written 11 days ago by ▴ 40
0
votes
1
reply
487
views
FASTQ files for 30x 1KGP of Phase 3 data
1000genomes fastq
updated 4 days ago by 41k • written 13 months ago by • 0
336 results • Page 1 of 7
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The Biostar Herald for Monday, December 11, 2023
Comment: GATK GetPileupSummaries Java heap space
The Biostar Herald for Monday, December 11, 2023
A: How To Sort Sam File
Answer: GATK GetPileupSummaries Java heap space
Answer: Autocompleting paths within scripts
Are Variable Features ranked in seurat?
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Recent Replies
Comment: How should I run ssgsea analysis ? by Ram 41k
Just add a statement to your comments stating that the text was generated using ChatGPT - it is a good tool but it's not aware of its own s…
Comment: Autocompleting paths within scripts by DanielEB_fisk ▴ 20
Yep, sorry, you are right it is not a bioinformatics question. I asked here because it relates with the work we do anyway.
Comment: autodock vina on mac by Ram 41k
That section is for after you have virtualbox set up. You may have to run a really old version of macOS within the virtualbox, so be prepar…
Comment: ChatGPT optimized for bioinformatics questions by Ram 41k
I understand. The purpose of my comment is to serve as feedback.
Comment: How can I obtain the DNA sequences of each CDS for several genbank files? by Ram 41k
Look into passing command line parameters to a python script. You can pass the input file name as a parameter to the script and execute the…
Answer: Autocompleting paths within scripts by Michael 53k
Not really a Bioinformatics question but generally very useful: [vim can do that][1] [type some prefix of path]<Ctrl-x><Ctrl-f> This…
Comment: How can I obtain the DNA sequences of each CDS for several genbank files? by Raphaëlle • 0
Hello, Thank you very much for your quick reply. That was indeed the issue! Another question: is there a simple way of automating this …
Answer: Cluster sub-set analysis using Seurat by j.gleixner ▴ 10
There now is also `Seurat::FindSubCluster`
Comment: How can i control the cluster number in scRNASeq clustering by Seurat package by j.gleixner ▴ 10
There is now also Seurat::BuildClusterTree that makes this easier.
Answer: How can i control the cluster number in scRNASeq clustering by Seurat package by j.gleixner ▴ 10
If you want to get a certain number of clusters without resorting to trying different settings for the resolution parameter, you can firs…
Answer: How to speed-up to contruct phylogenetic tree by Nelo ▴ 20
I will also try this `fasttree`
Comment: i ues schicexplorer's hicbuildmatrix code complains that two sam files do not ha by 1125195245 • 0
I tried using bowtie2's --reorder command to output a sam file for each of the two files, and then used both sam files to build the matrix,…
Comment: How to speed-up to contruct phylogenetic tree by Nelo ▴ 20
I used MEGA CC (comand line option) but there is no option to specify threads in its `--help` manual . And default thread is 4
Comment: How to speed-up to contruct phylogenetic tree by Nelo ▴ 20
The average length of fasta sequences is ~300aa length. I can't exclude any sequences as I have to provide them nomenclature aslo on the ba…
Comment: How to speed-up to contruct phylogenetic tree by Nelo ▴ 20
I used Raxml for a trial fasta file of about only 33 sequences as: `raxmlHPC-PTHREADS-AVX -f a -T 80 -m PROTGAMMAWAG -n test1 -s bittergou…
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