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4
replies
975
views
What to do when having differenet versions of ensembl IDs?
R Bioconductor RNA-Seq
updated 4.5 years ago by 13k • written 4.5 years ago by • 0
4
votes
6
replies
14k
views
Problem using a custom blast database in tblastx
blast software error
updated 4.5 years ago by • 0 • written 11.3 years ago by ▴ 290
0
votes
0
replies
970
views
GSEAPY Enrichr Question
enrichment
4.5 years ago by bcopeland64 • 0
0
votes
1
reply
4.7k
views
Blastx: FASTA-Reader: Ignoring invalid residues at position(s): On line 25975584
RNA-Seq assembly
4.5 years ago by nikhilshinde0909 • 0
0
votes
8
replies
1.1k
views
How to demultiplex SmartSeq2 run where settings were set to one index instead of two?
RNA-Seq sequencing
4.5 years ago by RhiRhiO • 0
0
votes
0
replies
549
views
MetaData extraction of Sequences
genome
4.5 years ago by inebrahim99 • 0
1
vote
4
replies
860
views
Time course data analysis
RNA-Seq NGS
4.5 years ago by Andrew Liu ▴ 10
9
votes
5
replies
8.9k
views
Simulating Rna-Seq Reads
rna alignment simulation
updated 4.5 years ago by 20 • written 14.8 years ago by ★ 2.7k
1
vote
1
reply
1.3k
views
Visualizing FIMO Output
FIMO RNA Motif Visualization
updated 4.5 years ago by 36k • written 4.5 years ago by • 0
11
votes
8
replies
14k
views
Question: Convert Ensembl Transcript Ids Ensmust To Gene Symbol In R
R ENSEMBL gene
updated 3.9 years ago by 89k • written 4.5 years ago by ▴ 150
0
votes
5
replies
1.6k
views
Convert absolute count into TPMs, merge exons or average gene length?
RNA-Seq gene
updated 4.5 years ago by ★ 30k • written 4.5 years ago by • 0
0
votes
3
replies
1.4k
views
clipOverlap from BamUtil modifies CIGAR string => error in GATK
rna-seq
updated 4.5 years ago by ▴ 20 • written 4.6 years ago by 9.3k
0
votes
0
replies
2.0k
views
"htsjdk.samtools.SAMFormatException: Error parsing text SAM file. Not enough fields" wrong message in the chromHMM run
chromHMM SAMFormatException
4.5 years ago by lhaiyan3 ▴ 80
3
votes
2
replies
4.2k
views
BLAST Global alignment
alignment blast+ dna blastn emboss
updated 4.5 years ago by 153k • written 4.5 years ago by ▴ 10
2
votes
3
replies
1.0k
views
How to remove repeats on galaxy
alignment repeats galaxy
updated 4.5 years ago by 20 • written 4.7 years ago by ▴ 70
0
votes
0
replies
922
views
Job: HIRING: Nanopore Production Specialist - UC Santa Cruz Genomics Institute
nanopore Genomics sequencing
updated 2.5 years ago by 45k • written 4.5 years ago by ▴ 30
2
votes
3
replies
1.5k
views
gencode gtf file derived geneID can't be annotated to gene symbol following Deseq2 manual
R RNA-Seq gene
4.5 years ago by Kai_Qi ▴ 130
1
vote
2
replies
2.6k
views
How to split Double or Multiple Nucleotide Polymorphisms (DNP) into Single Nucleotide Polymorphisms (SNP)?
SNP variant calling vcf
updated 4.5 years ago by 20 • written 8.4 years ago by ▴ 60
1
vote
5
replies
1.5k
views
qiaseq panel fastq to vcf
ngs qiaseq freebayes
4.5 years ago by tadeja.klade ▴ 10
4
votes
5
replies
2.8k
views
Whole blood single cell RNA-seq dataset?
RNA-Seq scRNA-Seq whole blood single cell
2.4 years ago by predeus ★ 2.1k
1
vote
7
replies
2.7k
views
lftp mput 530 Login incorrect
software error
4.5 years ago by leranwangcs ▴ 150
0
votes
0
replies
694
views
Is it possible to do an analysis of rna-seq of specific data from dataset or should I do the whole dataset?
RNA-Seq sequence next-gen
4.5 years ago by ashwing.kofficial ▴ 10
1
vote
1
reply
11k
views
Negative normalized Enrichment Score (NES) in GSEA analysis
GSEA
updated 3.1 years ago by 45k • written 9.8 years ago by ▴ 700
6
votes
10
replies
3.5k
views
Removing chrEBV reads from bam file
bam genome
updated 2.5 years ago by 45k • written 4.5 years ago by ▴ 810
3
votes
5
replies
4.8k
views
Problems with ArrayExpress datasets downloads on Bioconductor
arrayExpress bioconductor
updated 4.5 years ago by ▴ 60 • written 6.6 years ago by ▴ 120
0
votes
0
replies
878
views
News: Learn how to do modern reproducible data science
Snakemake Workflows Nextflow
updated 2.6 years ago by 45k • written 4.5 years ago by ★ 2.6k
0
votes
2
replies
3.0k
views
Variant calling 10x 3' scRNA data?
10x rna-seq RNA-Seq snp
4.5 years ago by scrnaresearch ▴ 10
0
votes
5
replies
1.8k
views
How to calculate p-values from PLINK output by hand
plink p-values
4.5 years ago by L_to_the_m ▴ 10
8
votes
9
replies
3.4k
views
BLASTP - HSPs and bitscores
BLASTP hsp bit-score
updated 4.5 years ago by 15k • written 4.5 years ago by ▴ 140
0
votes
0
replies
822
views
News: Noncoding RNA conference (including bioinformatics)
conference RNA noncoding-RNA
updated 2.6 years ago by 45k • written 4.5 years ago by ▴ 20
7
votes
19
replies
4.6k
views
DNA sequence complexity with a sliding window
R python dna
updated 4.5 years ago by 153k • written 4.5 years ago by ▴ 750
0
votes
1
reply
1.2k
views
Instrumental Variables and confounder in Mendelian Randomization
Variables Mendelian randomization Instrumental
4.5 years ago by Shicheng Guo ★ 9.6k
1
vote
1
reply
1.6k
views
Is there any problem on Mendelian Randomization analysis with binary exposure and outcome?
SNP
updated 4.5 years ago by • 0 • written 7.0 years ago by ▴ 10
2
votes
4
replies
3.2k
views
[OP Inactive] clusterProfiler (enrichKEGG) error
kegg clusterProfiler Guangchuang Yu
updated 4.5 years ago by 20 • written 7.5 years ago by ▴ 30
4
votes
6
replies
2.1k
views
Weird MAplot with DEGs lying along the diagonals
microarray maplot normalization agilent
updated 4.5 years ago by 13k • written 4.5 years ago by ▴ 20
0
votes
2
replies
1.6k
views
Searching for a free alternative to IPA
rna-seq ipa
4.5 years ago by francesca3 ▴ 160
0
votes
2
replies
1.3k
views
freebayes calls presumably homozygous variants as heterozygotes
SNP freebayes variant-call genotyping
updated 17 months ago by • 0 • written 4.5 years ago by • 0
1
vote
3
replies
1.4k
views
Mapping reads to contigs with BBMap - output statistics question (metagenome)
Assembly alignment Metagenome
4.5 years ago by bioknown • 0
0
votes
0
replies
656
views
How to select parameters for RNAplfold?
RNA-Seq rna-seq sequence
4.5 years ago by qwesxadzc9 • 0
1
vote
0
replies
824
views
Measuring Co-Occurrence of Gene Clusters (Bacteria)
antismash gene clusters co-occurrence
4.5 years ago by biohacker_tobe ▴ 80
4
votes
13
replies
5.0k
views
Creating a Contingency Table (Gene Absence Presence)
gene R microbes dataframe genome
4.5 years ago by biohacker_tobe ▴ 80
0
votes
0
replies
1.3k
views
Co-Occurrence Heatmap Creation
ggplot2 r R heatmap statistics
4.5 years ago by biohacker_tobe ▴ 80
6
votes
3
replies
7.8k
views
Co-Occurrence Network Graph & Statistics
R networks dataframe
4.5 years ago by biohacker_tobe ▴ 80
6
votes
3
replies
5.7k
views
Run R in multi threaded
R
updated 4.5 years ago by 89k • written 9.7 years ago by ▴ 990
0
votes
0
replies
615
views
need advice for comparing fragment counts of genes across multiple WGS metagenomes
WGS normalization KMA
4.5 years ago by sapuizait ▴ 10
0
votes
0
replies
841
views
Forum: Tools to check if the user defined pathway is enriched in the data
RNA-Seq sequencing R
updated 2.5 years ago by 45k • written 4.5 years ago by ▴ 60
1
vote
1
reply
2.2k
views
Why is my miRNA-seq mapping rate so low?
sequencing miRNA miRNA-seq RNA-Seq
4.5 years ago by cecilomar6 • 0
1
vote
3
replies
1.1k
views
How to include NCBI blastp while making an online database?
python database NCBI
updated 4.5 years ago by ★ 3.3k • written 4.5 years ago by ▴ 90
0
votes
3
replies
954
views
LeuceGene AML data Survival, Clinical and Mutation Data
RNA-Seq AML
4.5 years ago by onkarmulay10 • 0
0
votes
0
replies
832
views
tophat2 mapping fr-firststrand or fr-secondstrand ?
tophat2 fr-firststrand fr-secondstrand AB SOLiD
4.5 years ago by debitboro ▴ 270
121,910 results • Page 696 of 2439
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Comment: RNA-SEQ where only a subset of genes is of interest
Answer: GrCh37 or GrCh38? That is the question.
Answer: GrCh37 or GrCh38? That is the question.
GrCh37 or GrCh38? That is the question.
Best Practices/Softwares To Calculate Ka/Ks Ratio
A: Best Practices/Softwares To Calculate Ka/Ks Ratio
A: Best Practices/Softwares To Calculate Ka/Ks Ratio
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Recent Replies
Comment: RNA-SEQ where only a subset of genes is of interest by ATpoint 89k
Is this single-cell? How many genes are we talking about? > The alternative would be to just use the raw data without normalization, run W…
Comment: Developing a genomics ML model using bytes? by ATpoint 89k
So essentially you work on a compression algorithm, is it? If so, be sure to bechmark your idea against the hundreds of existing and fast c…
Comment: How to get a legend from genoplotR? by antonioggsousa 3.4k
Hi, I'm not familiar with this package or function, but from the function documentation that you had provided in the link, it says about …
Comment: Hifiasm is getting killed while trying to assemble a genome by Panos ★ 1.8k
I don't mean adapter contamination. I mean contamination of your sample with DNA from other organisms. In my previous lab, for example, we …
Comment: Developing a genomics ML model using bytes? by 1769mkc ★ 1.3k
how about fastq.gz?
Answer: Trouble when installing arb by SilentGene ▴ 120
I've got the same error when installing from `arb-6.0.6-source.tgz` and `arb-7.0-source.tgz`. Anyone has any solution?
Comment: Hifiasm is getting killed while trying to assemble a genome by pranavdatar01 • 0
Yes, I did check for adaptor contamination, and did not find any. I have kept all the reads with quality score of more than 30.
Comment: Hifiasm is getting killed while trying to assemble a genome by Panos ★ 1.8k
No overlapping reads? Have you checked for contamination?
Comment: Tried building a compact sequence format with 4-bit storage by Pranava ▴ 10
I see, but the reason I was planning on using a 4bit system is so that there wouldn't be too much data loss but thank you for the suggesti…
Comment: Splice junctions plots for long-read seq data by alison.ludzki • 0
Thank you! I will check out miso!
Comment: Hifiasm is getting killed while trying to assemble a genome by pranavdatar01 • 0
I did subsample the data to 30x coverage. I did run hifiasm on it, the log file did show some contents, but hifiasm ended again, stating th…
Comment: Tried building a compact sequence format with 4-bit storage by Alex Reynolds 36k
Using four bits for storage won't beat 2bit, of course, but direct access to a sequence of interest sounds interesting and useful and might…
Comment: Hifiasm is getting killed while trying to assemble a genome by Panos ★ 1.8k
Why don't you subsample your HiFi reads and try running hifiasm again? Maybe this will help if you have memory problems. However, I haven't…
Comment: Is total miRNA in EV constant? Implications for library size normalization. by Gordon Smyth ★ 8.3k
RNA-seq is very good at relative analyes. It would be straightforward to determine which miRNAs are relatively more abundant, compared to o…
Comment: Tried building a compact sequence format with 4-bit storage by Pranava ▴ 10
Woah!!! Thank you very much, Matthias. I honestly didn't even know some of those existed and I will definitely go through them and try to u…
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