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569 results • Page 2 of 12
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3
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7
replies
1.6k
views
align_and_estimate_abundance error Trinty
align_and_estimate_abundance RNA-SEQ RSEM Trinity
updated 22 days ago by 39k • written 20 months ago by ▴ 60
0
votes
1
reply
1.6k
views
project_tree_builder.exe not found, problem in configuring build tree of NCBI c++ toolkit
cpp toolkit blast NCBI
updated 15 days ago by 39k • written 7.4 years ago by ▴ 10
0
votes
0
replies
1.6k
views
mothur - stability.files does not contain sample group names
mothur software-error
updated 22 days ago by 39k • written 5.8 years ago by ▴ 20
5
votes
5
replies
1.6k
views
bio-newbie / gene research / tools and methods
methods research gene
updated 19 days ago by 39k • written 5.4 years ago by • 0
4
votes
8
replies
1.6k
views
How to extract promoter sequences from a plant draft genome?
promoter genome
updated 4 days ago by 39k • written 3.7 years ago by ▴ 100
1
vote
3
replies
1.5k
views
Using SeqAn and other external libraries in C++
Read-Mapping SeqAn
updated 20 days ago by 39k • written 5.6 years ago by ▴ 50
4
votes
6
replies
1.5k
views
Why weblogo of biopython doesn't work?
Biopython Weblogo
updated 5 days ago by • 0 • written 9 months ago by ▴ 20
0
votes
3
replies
1.5k
views
Converting a mutation data file into vcf?
next-gen-sequencing exome
updated 25 days ago by 39k • written 6.0 years ago by ▴ 20
1
vote
4
replies
1.5k
views
Time series event recurrence comparison
recurrence time-series
updated 7 days ago by 39k • written 6.7 years ago by 10k
0
votes
0
replies
1.5k
views
how to detect the presence of Integrative and conjugative elements in bacterial genome.
Genomics
updated 21 days ago by 39k • written 5.7 years ago by ▴ 180
2
votes
7
replies
1.5k
views
Technology Stack of NCBI (Genbank, GEO, etc.)
sequence ncbi gene genbank
updated 15 days ago by 39k • written 5.3 years ago by ▴ 70
0
votes
1
reply
1.5k
views
Why does shoremap calculate allele frequency this way?
shoremap allele-frequency
updated 20 days ago by 39k • written 5.7 years ago by ▴ 10
0
votes
8
replies
1.5k
views
Chromosome Location of Sequence in Fasta File using Biopython
biopython python
updated 21 hours ago by 39k • written 3.5 years ago by • 0
5
votes
4
replies
1.5k
views
Detection of DE genes among different tissues of an organism during time - RNA seq
detection DE-genes multi-treatments time-series
updated 7 days ago by 39k • written 6.9 years ago by ▴ 720
0
votes
0
replies
1.5k
views
CD-hit records matching and parsing
bash python cd-hit text-processing
updated 11 days ago by 39k • written 4.3 years ago by • 0
0
votes
5
replies
1.5k
views
terminal can't activate base automatically (conda)
conda
updated 26 days ago by 39k • written 22 months ago by ▴ 20
0
votes
5
replies
1.4k
views
Best Blast Hits from Tabular Outputs in Multiple files
python shell blast
updated 20 days ago by 39k • written 5.7 years ago by • 0
1
vote
2
replies
1.4k
views
Getting full list for DEGs in Noiseq
RNA-Seq
updated 19 days ago by 39k • written 5.4 years ago by ▴ 10
0
votes
0
replies
1.4k
views
envelope and alignment coordinates in hmmsearch result
hmmer sequence alignment hmmsearch
updated 11 days ago by 39k • written 4.4 years ago by • 0
1
vote
3
replies
1.4k
views
Is there any tool available for sequence alignment concatenation and supermatrix file generation other than Fastconcat-G?
Assembly alignment software-error
updated 1 day ago by 39k • written 3.6 years ago by ▴ 100
1
vote
3
replies
1.4k
views
How to check quality of multiple sequence alignment (MSA)?
MSA multiple-sequence-alignment R
updated 21 days ago by 39k • written 3.2 years ago by ★ 2.0k
2
votes
4
replies
1.4k
views
Gettin Consensus From Multiple Whole Genomes
multiple-sequence-alignment whole-genome-alignment
updated 21 days ago by 39k • written 6.4 years ago by • 0
0
votes
3
replies
1.4k
views
SNPEff not showing SNP
snpEff variant-annotation SNP
updated 15 days ago by 39k • written 5.1 years ago by • 0
0
votes
2
replies
1.4k
views
How to perform statistical analysis of label free experiment using results from Proteome Discoverer?
Proteome-Discoverer Label-Free Proteomics
updated 1 day ago by 39k • written 4.5 years ago by ▴ 80
1
vote
3
replies
1.4k
views
Alignment of two different file format
alignment
updated 21 days ago by 39k • written 5.8 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 25 days ago by 39k • written 6.0 years ago by ▴ 90
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 26 days ago by ▴ 690 • written 2.6 years ago by • 0
0
votes
0
replies
1.4k
views
How to use SABmark 1.65 as a benchmark?
multiple-sequence-alignment SABmark
updated 21 days ago by 39k • written 6.7 years ago by • 0
0
votes
1
reply
1.4k
views
Pipeline for scRNA-Seq
next-gen R RNA-Seq
updated 20 days ago by 39k • written 5.6 years ago by ▴ 10
1
vote
5
replies
1.3k
views
WGCNA Co-expression network analysis on cuffdiff output
wgcna cuffdiff
updated 13 days ago by 39k • written 4.7 years ago by ▴ 10
0
votes
4
replies
1.3k
views
File not found error on program installation.
samtools htslib Cpp
updated 15 days ago by 39k • written 3.6 years ago by ▴ 100
0
votes
3
replies
1.3k
views
Cannot open BAM files with the SeqAn library
cpp seqan Bam sequencing
updated 15 days ago by 39k • written 5.2 years ago by • 0
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 11 days ago by 39k • written 4.3 years ago by ▴ 240
3
votes
8
replies
1.3k
views
Kallisto mapping paired end
Kallisto mapping
updated 25 days ago by 39k • written 15 months ago by ▴ 20
3
votes
5
replies
1.3k
views
Trouble with best practices
samtools WES NGS GATK
updated 18 days ago by 39k • written 5.3 years ago by • 0
0
votes
0
replies
1.3k
views
Human Breast Cancer Panel QIAseq manifest
manifest panel
updated 22 days ago by 39k • written 5.9 years ago by ▴ 10
1
vote
0
replies
1.3k
views
NCBI Taxon ID to IMG Genome IDs
taxon html
updated 5 days ago by 39k • written 3.9 years 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 21 days ago by 39k • written 3.3 years ago by • 0
2
votes
4
replies
1.3k
views
hisat2 SyntaxError: invalid syntax
alignment hisat2
updated 22 days ago by 39k • written 19 months ago by ▴ 10
3
votes
4
replies
1.3k
views
fastPHASE -F provided to estimate haplotype frequencies, but no freqs in output
genomics phasing fastPHASE
updated 15 days ago by 39k • written 5.2 years ago by ▴ 10
0
votes
0
replies
1.3k
views
Cuffdiff with 2 conditions and time series
cuffdiff time-series RNA-Seq transcriptome
updated 7 days ago by 39k • written 6.2 years ago by • 0
1
vote
0
replies
1.2k
views
Align two single cell experiments
R single-cell
updated 12 days ago by 39k • written 4.5 years ago by ▴ 230
2
votes
3
replies
1.2k
views
mutational signatures in different tumor samples
somatic mutation mutational signature
updated 5 days ago by ★ 2.9k • written 4.4 years ago by ▴ 20
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 22 days ago by 39k • written 19 months ago by ▴ 10
0
votes
1
reply
1.2k
views
Best tool for bacterial genomic island prediction?
genome genomic-island
updated 6 days ago by 39k • written 4.0 years ago by ▴ 100
0
votes
0
replies
1.2k
views
Counting the number of paralogues for mouse genes gives me the wrong frequency
ensembl R biomart
updated 19 days ago by 39k • written 5.4 years ago by • 0
4
votes
5
replies
1.2k
views
Distributed / parallel computing in bioinformatics
distributed-computing
updated 22 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 15 days ago by 39k • written 4.8 years ago by ▴ 140
0
votes
4
replies
1.1k
views
No space separating sequence and name PopArt error !?
popart traits haplotypes python
updated 25 days ago by 39k • written 2.1 years ago by • 0
0
votes
0
replies
1.1k
views
EDGE microarray time series analysis fit_models() ERROR
microarray time-series
updated 7 days ago by 39k • written 5.4 years ago by ▴ 10
569 results • Page 2 of 12
Recent Votes
Answer: Extract sequences from a fastq file by a list of IDs
Answer: Extract sequences from a fastq file by a list of IDs
A: Collapse Repeated Reads
A: Extract Reads From A Bam File That Fall Within A Given Region
Comment: Masking before RNA-Seq Alignment and Gene Prediction in Plant Genomes
Comment: Alignment of case vs. control from different origin
A: understanding bedtools coverage output
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Recent Replies
Comment: Asking for feedback on a Python library for computing alignments by Alexander ▴ 70
Thanks for sharing ! It seems there is a problem to install on Kaggle cloud (like a Colab): I tried several ways: https://www.kaggle.com/co…
Comment: Masking before RNA-Seq Alignment and Gene Prediction in Plant Genomes by Darked89 4.4k
I am not sure what you gain by using hard masked genome for RNA-Seq mapping. There will be reads covering some introns. But if you mask rep…
Comment: Extract sequences from a fastq file by a list of IDs by mhpakdel96 • 0
Thanks a lot, it works
Comment: Differential protein expression analysis by dsull ★ 4.2k
I don't have a tutorial but see this paper I co-authored: https://pubs.acs.org/doi/abs/10.1021/acs.jproteome.0c00666 All of the upstream …
Comment: Differential protein expression analysis by Ribo ▴ 40
Thank you! Is there a recommended tutorial for proteomics analysis?
Comment: Limma returned only positive logFC values by melissachua90 ▴ 40
I clustered the samples into subtypes and am now comparing the differential expression across the subtypes.
Answer: Limma returned only positive logFC values by Gordon Smyth ★ 6.1k
No, your code isn't correct. You are testing one group mean equal to zero instead of testing for differences between two groups. I wonder w…
Answer: Extract sequences from a fastq file by a list of IDs by GenoMax 129k
Using `filterbyname.sh` from [**BBMap suite**][1]: You need to include the `/1` in the header in your list file (here I am using the `nam…
Comment: Limma returned only positive logFC values by melissachua90 ▴ 40
Yeah, I added the design matrix. `design <- model.matrix(~0+group)`. The `counts` is log2-normalized raw data.
Comment: Masking before RNA-Seq Alignment and Gene Prediction in Plant Genomes by Ayish • 0
Thank you for reply. I have Illumina paired-end reads. Would it be fine if I use hard-masking for STAR and soft-masked genome for BRAKER2? …
Comment: Masking before RNA-Seq Alignment and Gene Prediction in Plant Genomes by Darked89 4.4k
Soft masking the genome (unless something changed) not make any difference for STAR. Depending on how your RNA-Seq is done (Illumina? paire…
Answer: How to handle NaN in emmax Kinship matrix? by Thu • 0
Hi! Thanks for sharing your solution! It works! :)
Comment: Gene prediction software by Darked89 4.4k
Looks like there are five Clarias genomes: * https://www.ncbi.nlm.nih.gov/genome/?term=txid13012[Organism:exp] The most complete seems t…
Comment: Alignment of case vs. control from different origin by sativus ▴ 10
Again, thank you so much for these very clearly explained summaries. After reading some articles on the matter, i feel i have a much better…
Answer: Extract sequences from a fastq file by a list of IDs by colindaven 4.9k
Some people I know have used filter-fastq successfully: https://github.com/Floor-Lab/filter-fastq
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