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468 results • Page 2 of 10
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2
votes
4
replies
1.4k
views
Gettin Consensus From Multiple Whole Genomes
multiple-sequence-alignment whole-genome-alignment
updated 11 days ago by 39k • written 6.4 years ago by • 0
1
vote
3
replies
1.4k
views
How to check quality of multiple sequence alignment (MSA)?
MSA multiple-sequence-alignment R
updated 11 days ago by 39k • written 3.2 years ago by ★ 2.0k
0
votes
3
replies
1.4k
views
SNPEff not showing SNP
snpEff variant-annotation SNP
updated 5 days ago by 39k • written 5.1 years ago by • 0
1
vote
3
replies
1.4k
views
Alignment of two different file format
alignment
updated 11 days ago by 39k • written 5.7 years ago by • 0
6
votes
7
replies
1.4k
views
Bioinformatics Master Project With More Focus on Developing Algorithm and Software
Masters Algorithm Software
updated 15 days ago by 39k • written 6.0 years ago by ▴ 90
0
votes
0
replies
1.4k
views
How to use SABmark 1.65 as a benchmark?
multiple-sequence-alignment SABmark
updated 11 days ago by 39k • written 6.6 years ago by • 0
0
votes
1
reply
1.4k
views
Pipeline for scRNA-Seq
next-gen R RNA-Seq
updated 10 days ago by 39k • written 5.6 years ago by ▴ 10
0
votes
1
reply
1.4k
views
Extract sequence subset from multiple sequence alignment based on position in a specific species.
R Biostrings msa
updated 16 days ago by ▴ 690 • written 2.6 years ago by • 0
1
vote
5
replies
1.3k
views
WGCNA Co-expression network analysis on cuffdiff output
wgcna cuffdiff
updated 3 days ago by 39k • written 4.7 years ago by ▴ 10
1
vote
1
reply
1.3k
views
Can HISAT2 be invoked in bash shell, and can it be fed variables or names with wildcards as inputs?
Bash Shell HISAT2
updated 1 day ago by 39k • written 4.3 years ago by ▴ 240
0
votes
3
replies
1.3k
views
Cannot open BAM files with the SeqAn library
cpp seqan Bam sequencing
updated 5 days ago by 39k • written 5.2 years ago by • 0
0
votes
4
replies
1.3k
views
File not found error on program installation.
samtools htslib Cpp
updated 5 days ago by 39k • written 3.6 years ago by ▴ 100
0
votes
0
replies
1.3k
views
Human Breast Cancer Panel QIAseq manifest
manifest panel
updated 12 days ago by 39k • written 5.9 years ago by ▴ 10
3
votes
5
replies
1.3k
views
Trouble with best practices
samtools WES NGS GATK
updated 8 days ago by 39k • written 5.3 years ago by • 0
3
votes
8
replies
1.3k
views
Kallisto mapping paired end
Kallisto mapping
updated 15 days ago by 39k • written 15 months ago by ▴ 20
0
votes
4
replies
1.3k
views
How can I extract position information from multiple alignment format?
CLUSTAL MAFFT multiple-alignment
updated 11 days ago by 39k • written 3.3 years ago by • 0
3
votes
4
replies
1.3k
views
fastPHASE -F provided to estimate haplotype frequencies, but no freqs in output
genomics phasing fastPHASE
updated 5 days ago by 39k • written 5.2 years ago by ▴ 10
2
votes
4
replies
1.3k
views
hisat2 SyntaxError: invalid syntax
alignment hisat2
updated 12 days ago by 39k • written 19 months ago by ▴ 10
1
vote
0
replies
1.2k
views
Align two single cell experiments
R single-cell
updated 2 days ago by 39k • written 4.5 years ago by ▴ 230
0
votes
0
replies
1.2k
views
Counting the number of paralogues for mouse genes gives me the wrong frequency
ensembl R biomart
updated 9 days ago by 39k • written 5.3 years ago by • 0
0
votes
3
replies
1.2k
views
Ensemble file Mus_musculus.GRCm38.dna.primary_assembly.fa.gz unzipping to incorrect contents
genome RSEM Ensembl
updated 12 days ago by 39k • written 19 months ago by ▴ 10
4
votes
5
replies
1.2k
views
Distributed / parallel computing in bioinformatics
distributed-computing
updated 12 days ago by 39k • written 5.9 years ago by ▴ 710
1
vote
0
replies
1.2k
views
sequence alignment using edlib c++ library
cpp alignment
updated 5 days ago by 39k • written 4.8 years ago by ▴ 130
0
votes
0
replies
1.1k
views
Open source projects for canine genomics?
canine-genomics genomics
updated 11 days ago by 39k • written 5.7 years ago by • 0
0
votes
4
replies
1.1k
views
No space separating sequence and name PopArt error !?
popart traits haplotypes python
updated 15 days ago by 39k • written 2.0 years ago by • 0
0
votes
0
replies
1.1k
views
Adding annotation tracks for multiple alignment
visualization MAF multiple-alignment annotation
updated 11 days ago by 39k • written 4.7 years ago by ▴ 40
0
votes
2
replies
1.1k
views
What programatic skills necessary for biotechnologist
biotechnology perl python r
updated 15 days ago by 39k • written 6.3 years ago by • 0
0
votes
0
replies
1.1k
views
multiple Alignment Form
CIGAR multiple-alignment alignment
updated 11 days ago by 39k • written 6.6 years ago by ▴ 290
0
votes
0
replies
1.1k
views
Rearragement Scaffolds for Mutiple Sequence Alignment
multiple-sequence-alignment Post-assembly
updated 11 days ago by 39k • written 5.8 years ago by • 0
0
votes
1
reply
1.1k
views
Mauve export similarity
multiple-sequence-alignment mauve
updated 11 days ago by 39k • written 4.8 years ago by ★ 1.5k
3
votes
6
replies
1.1k
views
how to get total read count, mapped read count and unmapped read count from multiple sam or bam files
RNAseq PYTHON R bash
updated 11 days ago by 39k • written 2.7 years ago by ▴ 430
0
votes
2
replies
1.0k
views
Error in read.table(file = file, header = header, sep = sep, quote = quote, : duplicate 'row.names' are not allowed
URL R
updated 12 days ago by 39k • written 19 months ago by ▴ 80
0
votes
0
replies
1.0k
views
Annotate multiple rRNAs with variable and constant regions
rRNA multiple-alignment SILVA
updated 11 days ago by 39k • written 5.9 years ago by ★ 1.9k
0
votes
6
replies
1.0k
views
How do I tell piRNA population suppress TEs in a bed file?
mapping piRNAs TEs
updated 3 days ago by 39k • written 4.8 years ago by ▴ 110
0
votes
0
replies
987
views
FRMA processing on two different datasets of affy u133A not same dimensions
u133A R frma affy
updated 1 day ago by 39k • written 4.2 years ago by ▴ 10
0
votes
3
replies
985
views
Explanation? Read depth, quality, and assembly accuracy in Methylome analysis context
Assembly genome methylation
updated 1 day ago by 39k • written 4.3 years ago by ▴ 10
1
vote
1
reply
984
views
cfDNA target seq vs. cfDNA WES
cfDNA
updated 3 days ago by 39k • written 4.9 years ago by ▴ 40
1
vote
3
replies
982
views
BLAST: overflow error
BLAST
updated 15 days ago by 39k • written 13 months ago by ▴ 50
0
votes
0
replies
980
views
Python AttributeError: can't set attribute
Python
updated 15 days ago by 39k • written 15 months ago by • 0
0
votes
0
replies
959
views
Standalone Blast result customization
taxonomic-assignments
updated 11 days ago by 39k • written 5.8 years ago by • 0
1
vote
4
replies
956
views
Simulate the sequence data
next-gen-sequencing genetics
updated 5 days ago by 39k • written 5.1 years ago by ▴ 80
0
votes
5
replies
941
views
Bioinformatics conference with possible publication
conference
updated 2 days ago by 39k • written 4.6 years ago by ▴ 550
0
votes
3
replies
939
views
Sorting by Prefix Reversal (or Flipping Pancakes) approximation
algorithms
updated 2 days ago by 39k • written 4.5 years ago by • 0
1
vote
0
replies
936
views
can the differences in the protein sequence be ranked according to their relevance to a certain stimuli, using a statistical method when the protein …
sequence proteins
updated 12 days ago by 39k • written 5.9 years ago by ▴ 70
0
votes
1
reply
931
views
Questions about assembly of large metagenomics dataset
assembly metagenomics megahit
updated 2 days ago by 39k • written 4.5 years ago by • 0
1
vote
1
reply
927
views
microarray data handling
R microarray
updated 9 days ago by 39k • written 5.4 years ago by • 0
0
votes
2
replies
926
views
what do you mean by segment pairs
rna protein
updated 1 day ago by 39k • written 4.3 years ago by ▴ 50
6
votes
9
replies
925
views
Error when runing Bowtie2: (ERR): bowtie2-align exited with value 1
BAM Bowtie
updated 16 days ago by 39k • written 4 months ago by ▴ 40
0
votes
1
reply
899
views
Error: long vectors not supported yet in Monocle 2
Monocle Monocle2
updated 15 days ago by 39k • written 17 months ago by • 0
0
votes
0
replies
879
views
Using phosphonormalizer in phosphoproteomics experiments
phosphonormalizer phosphoproteomics Normalization
updated 12 days ago by 39k • written 5.9 years ago by • 0
468 results • Page 2 of 10
Recent Votes
Answer: Counting intronic reads in bulk RNA-seq
Answer: IGV displays genomic coordinates in a 1-based system or 0-based?
RNAseq expression data log2 transformed has negative values.
Samtools: "Too Many Open Files"
Filtering bad quality probes in illumina microarray data
gene filtering for agilent microarray using Limma
A: Identification Of Significant Differences Between Phylogentic Trees Using Distan
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Recent Replies
Comment: Error while running Megahit by Mensur Dlakic ★ 23k
We can't even begin to guess what the problem was without an error message.
Comment: DEgs RNAseq by dsull ★ 4.2k
Is this single-cell RNAseq or non-single-cell RNAseq? For single-cell, you typically don't do standard "differential gene expression analy…
Comment: Counting intronic reads in bulk RNA-seq by dsull ★ 4.2k
Correct, and I agree -- reads lying fully within introns are usually not counted for either single-cell or bulk. Inclusion of introns in a…
Answer: Counting intronic reads in bulk RNA-seq by swbarnes2 13k
Are you sure this is appropriate for bulk RNASeq? I thought intronic reads for single cell were only counted in nuclear preps.
Answer: Single cell chemistry by swbarnes2 13k
Are you sure these samples are 10x? How likey is it that the sequencing group messed up and ran the samples wrongly?
Comment: How to deal with duplicated gene IDs in TCGA RNA expression data? by Vincent Laufer ★ 2.8k
are they distinct transcript IDs but the same gene ID? can you provide any additional context?
Comment: SyntaxError (Perhaps you forgot a comma?) in snakefile when running FastQC. by Dhatri Badri • 0
that didn't work either
Answer: Why are some WES VCFs larger than others? by Vincent Laufer ★ 2.8k
Hi @kermit and prash (and others)! Nice discussion. I wanted to offer some **biological rationales** in addition to the technical reasons …
Answer: SyntaxError (Perhaps you forgot a comma?) in snakefile when running FastQC. by WouterDeCoster 47k
There is no `:` after `rule fastqc`
Comment: SyntaxError (Perhaps you forgot a comma?) in snakefile when running FastQC. by Dhatri Badri • 0
sorry that was a typo while i was copying my code! I still get the same error
Comment: too many zeros in 16S rRNA amplicon sequencing data by andres.firrincieli 3.3k
You have too many ASV (40k) and I think this is a problem related to the denoising (DADA2) of NovaSeq 6000 sequencing data. Maybe this post…
Answer: SyntaxError (Perhaps you forgot a comma?) in snakefile when running FastQC. by Pierre Lindenbaum 154k
> fastq.gz". what is the dot after `fastq.gz" ` ?
Comment: DownsampleSam by Pierre Lindenbaum 154k
1) I think this is just a warning 2) there must be another error displayed 3) look at samtools view --subsample 4) don't use loops but use…
Comment: ABySS genome assembler by npavliukovec • 0
Hello, yes, I tried it, but I have to do my home work on university's remote computer, unfortunatelly I go an error, when I try to use abys…
Comment: desgin a primer for CDS by yuxiang • 0
how can you know the primer is not bind to other gene site? how can you desgin an experiment? I use the FISH to identify the gene, how abo…
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