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9
votes
13
replies
15k
views
Sort bam file by coordinates using samtools
next-gen-sequencing gene rna-seq
updated 9 months ago by 43k • written 5.6 years ago by ▴ 30
3
votes
16
replies
11k
views
combining z-scores into a single z-score value
excel R statistics
updated 10 months ago by 43k • written 5.1 years ago by ▴ 60
0
votes
8
replies
9.9k
views
how to find a read by name in a bam file
next-gen-sequencing
updated 9 months ago by 43k • written 6.8 years ago by • 0
7
votes
8
replies
8.9k
views
Determining read count
trimmomatic rna-seq trinity
updated 7 months ago by 43k • written 8.0 years ago by ▴ 110
4
votes
12
replies
7.7k
views
6 follow
BWA error: no ID within the read group line
bwa readgroups RG parallel
updated 9 weeks ago by ▴ 10 • written 3.3 years ago by ▴ 60
2
votes
9
replies
7.5k
views
6 follow
Read MAP and PED files in PLINK
GWAS PLINK
updated 3 months ago by 141k • written 5.9 years ago by • 0
0
votes
7
replies
7.2k
views
Problem in in alignment by muscle
sequence muscle alignment
updated 9 months ago by 43k • written 6.7 years ago by ▴ 70
5
votes
5
replies
7.2k
views
Converting scRNA-Seq to Bulk-RNASeq
scRNASeq bulk-RNASeq RNA-Seq single-cell
updated 5 days ago by • 0 • written 3.8 years ago by ★ 1.8k
6
votes
4
replies
6.4k
views
What is gnomAD allele frequency
AF gnomAD
updated 3 months ago by ▴ 760 • written 3.0 years ago by ▴ 50
3
votes
7
replies
6.3k
views
Human reference files in HG38 GATK resource bundle
VCF
updated 10 months ago by ★ 4.3k • written 6.2 years ago by ▴ 970
3
votes
7
replies
6.3k
views
running trimmomatic inside Trinity
Assembly Trinity RNA-seq trimmomatic
updated 9 months ago by 43k • written 8.0 years ago by ▴ 50
2
votes
14
replies
5.9k
views
Using sam-dump in SRA toolkit to download chr20.bam from NA12878
sratoolkit sam-dump
updated 9 months ago by 43k • written 7.0 years ago by ▴ 10
0
votes
4
replies
5.8k
views
using IGV to visualize RNA seq alignment to transcriptome
rna-seq igv alignment
updated 7 months ago by 43k • written 7.8 years ago by ▴ 110
3
votes
14
replies
5.8k
views
remote command line BLAST job ends in CPU error and gives MBEDTLS version mismatch
blastn mbedtls blast linux blast+
updated 12 weeks ago by ▴ 40 • written 3.1 years ago by • 0
0
votes
4
replies
5.8k
views
Calculate Radius of Gyration [python 3]
biopython PDB Radius of Gyration python protein
updated 10 months ago by • 0 • written 6.4 years ago by ▴ 30
1
vote
5
replies
5.8k
views
Generate VCF File from Bam file and fasta by GATK
vcf SNP genome next-gen
updated 9 months ago by 43k • written 6.7 years ago by ▴ 70
0
votes
3
replies
5.6k
views
Bedgraphtobigwig Conversion Difficulties
bigwig
updated 9 months ago by 43k • written 11.1 years ago by • 0
1
vote
4
replies
5.5k
views
Conditionally coloring the fold change values to plot a heatmap using pheatmap
R heatmap
updated 11 months ago by 43k • written 6.1 years ago by ▴ 60
0
votes
9
replies
5.4k
views
Calculating FPKM and TPM by hand from htseq-count output?
RNA-Seq rna-seq htseq FPKM TPM
updated 8 months ago by 81k • written 5.0 years ago by ▴ 210
0
votes
1
reply
5.3k
views
Hapmap to vcf
vcf hapmap
updated 9 months ago by 43k • written 5.6 years ago by ▴ 150
0
votes
4
replies
5.3k
views
Sequence alignment length
multiple-sequence-alignment
updated 11 months ago by 43k • written 7.2 years ago by ▴ 20
0
votes
8
replies
5.2k
views
8 follow
cellranger mkref failed
next-gen-sequencing software-error RNA-seq
updated 6 days ago by • 0 • written 4.7 years ago by ▴ 180
2
votes
11
replies
5.2k
views
How long it takes to run repeat masker on a full genome
Assembly
updated 3 months ago by ▴ 190 • written 7.8 years ago by ▴ 20
3
votes
4
replies
5.2k
views
What does this Warning in HTSeq-count means? (Warning: Mate pairing was ambiguous)
RNA-Seq
updated 8 months ago by ▴ 10 • written 8.6 years ago by ★ 1.4k
7
votes
7
replies
4.9k
views
RNA-Seq time series analysis using a DESeq2 spline approach yields far too many significant genes
splines DESeq2 time-series RNA-Seq
updated 10 months ago by 43k • written 5.3 years ago by ▴ 80
10
votes
14
replies
4.9k
views
ATAC-seq data and deepTools: Small detail with impact on output
bigwig read-length deeptools ATAC-seq
updated 10 months ago by 43k • written 4.2 years ago by ▴ 50
1
vote
4
replies
4.8k
views
TCGA data(RPKM) differential gene expression
rna-seq R TCGA RPKM IPA
9 months ago by realnewbie ▴ 30
3
votes
2
replies
4.7k
views
How to plot a circular clustered heatmap with dendrogram
circular heatmap
updated 8 months ago by ▴ 30 • written 4.4 years ago by ▴ 180
2
votes
7
replies
4.6k
views
SRA toolkit internet settings
sratoolkit fastq-dump sequencing RNA-Seq
updated 9 months ago by 43k • written 7.7 years ago by ▴ 90
0
votes
8
replies
4.4k
views
Downloading single cell data from NCBI
ncbi rna-seq fastq-dump single-cell
updated 7 months ago by 43k • written 5.3 years ago by ▴ 380
0
votes
7
replies
4.4k
views
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 4 months ago by 43k • written 5.9 years ago by • 0
1
vote
0
replies
4.4k
views
how to convert .geno/.snp/.ind to .bed/.bim/.fam (ped plink format) in Windows
plink genomes ancestrymap
updated 9 months ago by 43k • written 7.8 years ago by ▴ 10
3
votes
4
replies
4.3k
views
Atypical volcano plot RNA-seq
volcano-plot RNA-seq deseq2
updated 7 months ago by 43k • written 5.4 years ago by ▴ 20
7
votes
13
replies
4.3k
views
6 follow
Is trimming necessary for RNAseq?
RNA-Seq trimming fastqc
updated 5 months ago by 81k • written 3.4 years ago by ▴ 10
1
vote
9
replies
4.3k
views
Unable to install bioconda and bowtie
bioconda conda
updated 4 months ago by 13k • written 18 months ago by ▴ 30
7
votes
8
replies
4.2k
views
DEseq2 design matrix with 3 factors
RNA-seq deseq2
updated 10 months ago by 43k • written 3.9 years ago by ▴ 60
11
votes
22
replies
4.1k
views
No significant DEG: A request to double check my commands for limma.
limma differential-gene-expression
updated 7 days ago by 43k • written 5.0 years ago by ▴ 260
0
votes
4
replies
4.1k
views
What is Dunn's multiple comparison test?
statistics
updated 11 months ago by 43k • written 6.6 years ago by • 0
3
votes
4
replies
4.1k
views
What are the Pros and Cons of working in Bioinformatics???
career bio
updated 11 months ago by 43k • written 6.2 years ago by ▴ 20
3
votes
6
replies
4.1k
views
how do Differential gene expression analysis by Salmon output
differential-gene-expression Salmon
updated 7 days ago by 43k • written 5.5 years ago by ▴ 100
1
vote
7
replies
4.0k
views
Adjust width of annotations in pheatmap
R heatmap
updated 6 months ago by 87k • written 5.4 years ago by ▴ 30
2
votes
4
replies
4.0k
views
Transcriptomic Coordinate Bam To Genomic Coordinate Bam
bam genomics
updated 9 months ago by 43k • written 11.3 years ago by ▴ 80
1
vote
5
replies
4.0k
views
Time-series or pairwise comparison EdgeR - what's more suited?
DGE-analysis Time-series pairwise
updated 10 months ago by 43k • written 7.6 years ago by ▴ 470
5
votes
19
replies
3.9k
views
8 follow
Hisat2 aligner problem
RNA-Seq ChIP-Seq alignment Assembly software error
updated 3 months ago by 81k • written 4.9 years ago by ▴ 340
0
votes
5
replies
3.9k
views
Phylogeny Heatmap with Python
multiple-sequence-alignment
updated 11 months ago by 43k • written 5.1 years ago by • 0
1
vote
8
replies
3.8k
views
No gene can be mapped
R GSEA
updated 3 months ago by ★ 1.8k • written 2.3 years ago by • 0
0
votes
16
replies
3.8k
views
Gff to genbank - feature is missing
DNA augustus gff3 genbank
updated 10 months ago by 43k • written 5.9 years ago by ▴ 10
0
votes
7
replies
3.7k
views
MUMmer plot visualization
MUMmer plot
updated 8 weeks ago by • 0 • written 3.2 years ago by ▴ 90
2
votes
4
replies
3.7k
views
Converting different annotation file formats (GTF/GFF/BED) to each other
rna-seq next-gen
updated 6 months ago by ▴ 120 • written 6.6 years ago by ▴ 150
10
votes
7
replies
3.7k
views
What is Pathway Analysis?
database analysis ontology pathway
updated 10 months ago by 43k • written 8.0 years ago by ▴ 330
1,000 results • Page 1 of 20
Recent Votes
Comment: RNAseq of primary tumor and metastases in two different organ
Comment: Bioinformatics_where do i start
Comment: Can I compare kallisto counts from samples with different amount of reads?
Comment: RNAseq of primary tumor and metastases in two different organ
Comment: CombineGVCFs vs. MergeVcfs
Comment: Bioinformatics_where do i start
Answer: Bwa sampe - BGI
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Recent Replies
Comment: SnpEff annotates coding duplication as intronic? by Ram 43k
Can you show us the output from VEP and snpEff? They could be annotating two different transcripts. EDIT: I ran VEP quickly on this varian…
Comment: Help/Direction Needed for Data Analysis of RNA by dsull ★ 5.8k
Honestly, any popular aligner will do: STAR, bowtie2, bwa, etc. Just make a FASTA file containing your sequences of interest, build an inde…
Comment: Rename multiple fastq.gz files by Jérémie • 0
Thank you! Just a stupid question, when I run this command it gives me the list of the names expected but does not actually change the name…
Comment: RNAseq of primary tumor and metastases in two different organ by BioinfGuru ★ 1.6k
That's normal. Anything lower than the lower limit of R's numerical value range is rounded to 0. No resolution is required. Just be careful…
Comment: Rename multiple fastq.gz files by bk11 ★ 2.3k
This will be a very rough way of doing it- #listing the fastq files ls *fastq.gz JM1-44589688_S693_L001_R1_001.fastq.gz JM110-…
Comment: RNAseq of primary tumor and metastases in two different organ by matteo.levorato • 0
on top of this I have many genes with a padj equal to zero, is this coming from an error or it's just that the value is too small for RStud…
Comment: Bwa sampe - BGI by ATpoint 81k
Honestly, use bwa mem like everyone else and call it a day. bwa mem ref.fa X1.fq.gz X_2.fq.gz | samtools sort -o sorted.bam See the b…
Comment: Bwa sampe - BGI by lorena9132 • 0
Hello, thank you very much for your response. I was referring more to using these options: -a INT Maximum insert size for a read pair …
Comment: gene body coverage with RSeqQC by BioinfGuru ★ 1.6k
Take a look at [this post][1] ... it might give a clue. Alternatively, for my installation the qcmodule is located at: /home/bioinfguru/…
Comment: Bioinformatics_where do i start by BioinfGuru ★ 1.6k
The [biostars handbook][1] is well worth the money [1]: https://www.biostarhandbook.com/
Comment: Statistical Advice Needed for RNAseq Data Analysis by David • 0
Thank you @atpoint for your reply, but I think I didn't explain myself clearly. Initially, I compared my two datasets to their control and …
Comment: RNAseq of primary tumor and metastases in two different organ by BioinfGuru ★ 1.6k
Most advise to avoid For Loops in R (don't ask me why, unexpected results and behaviours, poor efficiency I think). I would use tidyverse f…
Comment: RNAseq of primary tumor and metastases in two different organ by BioinfGuru ★ 1.6k
P-values are not corrected for the multiple comparisons inherent in differential gene expression analysis. FDR (aka qvalue) is used for sel…
Comment: CombineGVCFs vs. MergeVcfs by Jeremy Leipzig 22k
in the supplemental materials of that UKBB paper they actually do mention MergeVcfs but it must be a typo
Comment: add INFO tag to vcf with bcftools by Javier • 0
Hi, I'm trying to do something similar, could you share the code to do what you describe. Thanks
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