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122,217 results • Page 733 of 2445
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2.0k
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interpolation y vector
sequencing samtools bam matlab
updated 3.6 years ago by 45k • written 10.8 years ago by • 0
0
votes
1
reply
1.0k
views
APT rma-sketch gene has same values as exon - Affymetrix Human Exon 1.0 ST Array
APT exon-array
updated 4.8 years ago by ★ 90k • written 4.8 years ago by ▴ 40
0
votes
0
replies
1.6k
views
What is the criteria for defining a CRAPome cut-off score for filtering proteomics datasets?
crapome proteomics filtering cut-off score
4.8 years ago by Farah ▴ 80
0
votes
3
replies
1.2k
views
cant make index file for Wheat accepted_hits.bam file
RNA-Seq sequencing rna-seq
updated 4.8 years ago by 154k • written 4.8 years ago by • 0
0
votes
0
replies
653
views
Modelling Enzyme Effects on Molecules
modelling enzymes molecule TRITON
4.8 years ago by skizzy • 0
0
votes
11
replies
2.5k
views
Error when trying to convert BAM file to FASTQ.
samtools bedtools
4.8 years ago by DNAngel ▴ 260
2
votes
5
replies
1.6k
views
Howto transfer all 'product' qualifiers from a genbank file to another one
genbank biopython
4.8 years ago by a99942 • 0
0
votes
1
reply
1.2k
views
How to interpret Site Frequency Spectrum? (SFS, allele frequency spectrum)
snp SNP sequence gene
4.8 years ago by jaredmeyers • 0
5
votes
9
replies
5.8k
views
Error when trying to run IGV on server
igv
updated 4.3 years ago by ▴ 140 • written 6.2 years ago by ▴ 180
5
votes
5
replies
4.4k
views
Can featureCounts use sortedbycoordinate files?
RNA-Seq
updated 2.4 years ago by • 0 • written 4.8 years ago by ▴ 10
5
votes
4
replies
2.1k
views
Running blast shell script within python pipeline
sequence blast biopython
updated 4.8 years ago by 22k • written 4.8 years ago by ▴ 70
0
votes
2
replies
1.2k
views
Job: TENURE-TRACK OR TENURE-ELIGIBLE INVESTIGATOR IN CLINICAL DATA SCIENCE
Biostatistics Clinical-Informatics
updated 2.7 years ago by 45k • written 4.8 years ago by • 0
2
votes
5
replies
1.1k
views
anyway to save contaminated samples?
RNA-Seq
4.8 years ago by demoraesdiogo2017 ▴ 120
0
votes
2
replies
990
views
Drastic changes in sequencing saturation
next-gen sequencing
4.8 years ago by prosomething • 0
0
votes
0
replies
794
views
TypeError: '<' not supported between instances of 'str' and 'int' using fastq-dump
software error sequencing
4.8 years ago by a.krassnig ▴ 20
0
votes
3
replies
1.5k
views
Job: Bioinformatician Technical Lead, Kinomica Limited. Alderley Park, Cheshire, UK
LC-MSMS phosphoproteomics R cell-signalling
updated 2.5 years ago by 45k • written 4.8 years ago by • 0
0
votes
0
replies
921
views
Need to fix .sqn genome annotation file prior to uploading to NCBI
sqn NCBI
updated 2.2 years ago by 45k • written 4.8 years ago by ▴ 180
0
votes
0
replies
814
views
Applying Causal Discovery methods (CIT) on log transformed tpm data vs log transformed DESeq normalized data have differences why ?
causal discovery DESeq CIT
updated 4.8 years ago by 20 • written 4.8 years ago by • 0
0
votes
1
reply
1.3k
views
limma analysis when only Cy5 was used
two-channel-array limma gpr
updated 2.7 years ago by 45k • written 4.8 years ago by • 0
3
votes
2
replies
3.3k
views
Understanding Resource Job Allocation
snakemake slurm memory workflow
updated 4.8 years ago by 22k • written 4.8 years ago by ▴ 20
0
votes
0
replies
515
views
copy number variation
RNA-Seq
4.8 years ago by Rob ▴ 180
0
votes
1
reply
2.6k
views
Pairwise distance matrix using biopython
python phylogentics biopython
4.8 years ago by Elephantdumbo ▴ 20
7
votes
12
replies
4.0k
views
How to extract fasta headers that contains specific text and it's sequence
barrnap 16srRNA fasta
written 4.8 years ago by ▴ 190
0
votes
0
replies
1.0k
views
Job: Postdoctoral Fellowship in Metagenome Workflow Development and Analysis
Training Assembly Metagenome Microbiome sequencing
updated 2.5 years ago by 45k • written 4.8 years ago by • 0
10
votes
16
replies
45k
views
6 follow
Beginner in Python- need in assistance translating DNA into protein sequence
python
updated 4.8 years ago by • 0 • written 9.0 years ago by ▴ 10
0
votes
2
replies
2.4k
views
the difference between pysam and pybam
sequencing alignment
updated 4.8 years ago by 90k • written 4.8 years ago by ▴ 30
0
votes
0
replies
949
views
Calling UTRs in TCGA dataset
TCGA cancer UTR ORF
4.8 years ago by Jamie Watson ▴ 20
2
votes
5
replies
4.6k
views
Merge two columns by having alternating rows
R Rstudio Dataframe
updated 4.8 years ago by 13k • written 4.8 years ago by • 0
0
votes
0
replies
705
views
ICGC simple somatic mutations
snp
4.8 years ago by amenshamim • 0
0
votes
0
replies
1.3k
views
Automatize RMSD on PyMol
Python PyMol RMSD Structure
4.8 years ago by Bubu1208 • 0
0
votes
0
replies
661
views
Difference between run and SRA accession
SRA NCBI
4.8 years ago by n.mekkes • 0
0
votes
4
replies
2.5k
views
Use bowtie2 to assess the trinity assembly results, getting a strange results.
rna-seq assembly
updated 4.8 years ago by 35k • written 4.8 years ago by • 0
0
votes
10
replies
3.2k
views
Too many Terms after Enrichment analysis
GO enrichment analysis Slim
4.8 years ago by biosjm • 0
1
vote
9
replies
1.9k
views
cant find gene_id
RNA-Seq software error
4.8 years ago by meisam.radfar • 0
3
votes
5
replies
2.1k
views
Running purge_dups on a hybrid assembly (optical mapping + reads)
pacbio purge_dups Assembly bionano
updated 2.2 years ago by 8.1k • written 4.8 years ago by ▴ 350
0
votes
0
replies
682
views
Annovar Set ID
next-gen
4.8 years ago by storm1907 ▴ 30
1
vote
1
reply
1.1k
views
Bowtie2 ABRT error
RNA-Seq alignment sequencing software error
updated 4.8 years ago by 90k • written 4.8 years ago by • 0
1
vote
1
reply
3.2k
views
Is HISAT2 able to output only the best alignment?
HISAT2
updated 4.8 years ago by 20 • written 7.2 years ago by ▴ 10
2
votes
4
replies
1.5k
views
COVID-19 analysis pipelines
DNA-seq COVID-19 pipeline illumina
updated 4.8 years ago by 154k • written 4.8 years ago by ▴ 130
4
votes
4
replies
2.2k
views
WTF with the ensembl human genome?
genome ensembl refseq
updated 4.5 years ago by 154k • written 4.8 years ago by 9.3k
5
votes
5
replies
2.6k
views
Why VEP doesn't take strand into account?
vep ensembl snp
updated 4.8 years ago by 24k • written 4.8 years ago by ▴ 30
0
votes
0
replies
669
views
error in cummeRbund
RNA-Seq R gene
updated 4.8 years ago by 16k • written 4.8 years ago by ▴ 20
1
vote
2
replies
1.4k
views
Variant data from covid-19 patients
covid-19 vcf
updated 4.8 years ago by 24k • written 5.5 years ago by ▴ 110
0
votes
1
reply
865
views
Get overlapping features with certain fraction max
genome bedtools
updated 4.8 years ago by 166k • written 4.8 years ago by ▴ 90
4
votes
3
replies
3.3k
views
Michigan Imputation Server - typed-only sites?
imputation SNP genotyping michigan vcf
updated 4.8 years ago by • 0 • written 5.7 years ago by ▴ 180
4
votes
4
replies
1.3k
views
question about R language 'for' loop
RNA-Seq sequencing next-gen R gene
updated 4.8 years ago by ★ 1.4k • written 4.8 years ago by • 0
3
votes
3
replies
1.7k
views
Alignment to scRNA-seq data
RNA-Seq rna-seq alignment genome
updated 4.8 years ago by ★ 30k • written 4.8 years ago by • 0
0
votes
1
reply
1.0k
views
List of all promoter position
gene
updated 4.8 years ago by 13k • written 4.8 years ago by ▴ 90
2
votes
6
replies
1.4k
views
reduce speed terminal command submission
terminal macos bwa
updated 4.8 years ago by 45k • written 4.8 years ago by ▴ 10
0
votes
0
replies
633
views
Programs for analyze microarray results
genome
4.8 years ago by khanhlpbao • 0
122,217 results • Page 733 of 2445
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Comment: circos plot for genomic features
Answer: How to perform GO enrichment in non-model organisms?
Comment: circos plot for genomic features
Answer: How excactly is the Q30 is calculated?
A: PCA in a RNA seq analysis
what cause poly-G from NextSeq
what cause poly-G from NextSeq
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Recent Replies
Comment: Issue while running Kenddata. by GenoMax 154k
Look inside the `*.log` files to see if you can get additional clues (and post them here, if you can't figure out things). Check for lines …
Comment: Question about QC and scrublet by Arup Ghosh 3.5k
You can run Scrublet before filtering cells with high gene counts and compare the doublet score vs `n_counts_genes`.
Answer: How to perform GO enrichment in non-model organisms? by lieven.sterck 16k
In first instance you will as you say need to assign GOterms to your genes. eggNOG-mapper is certainly a valid approach to do this indeed. …
Comment: circos plot for genomic features by Matteo Ungaro ▴ 140
@colindaven thanks a lot! `clinker` also seems to be a nice/effective tool to do so. It happens we stuble across a work where they used `Ci…
Comment: circos plot for genomic features by colindaven 8.1k
Why not use something like Jbrowse2 instead ? https://jbrowse.org/jb2/gallery/ You can load both haplotypes, use minimap2 to create a paf …
Comment: How excactly is the Q30 is calculated? by colindaven 8.1k
This is really a question for your instrument provider. Only MGI application specialists and their bioinformaticians can really answer this…
Answer: How excactly is the Q30 is calculated? by GenoMax 154k
[**Phred quality scores**][1] have been in use since the 1990s and early days of human genome project. They were co-opted in the fastq form…
Comment: best practice for diploid variant calling by Matteo Ungaro ▴ 140
@kevin thanks I was experimenting with the following since I already pursued most of the approaches you mentioned and, in practice, they ar…
Answer: Chip-seq analysis Diffbind by ATpoint 90k
I think the results are expected. a) n=2 is underpowered, for any assay and in particular for ChIP-seq which has considerable noise. b) you…
Comment: low quality data or file name swapping -- cellranger arc errors when processing by Wu-Sheng Zhang ▴ 10
Hi @arup , after changing the file name following the read length, I can process them using cellranger arc successfully. Thank you very muc…
Comment: Visualize methylation status in Pacbio Hifi read by cmdcolin ★ 4.4k
(as the JBrowse dev) I'm glad to hear this. if you see any trouble with it feel free to let me know, I have tried to keep up to date with m…
Comment: low quality data or file name swapping -- cellranger arc errors when processing by Wu-Sheng Zhang ▴ 10
Got it! I will try to switch their name and re-run the cellranger arc. Thank you very much, @arup !
Answer: low quality data or file name swapping -- cellranger arc errors when processing by Arup Ghosh 3.5k
The barcode files with 24nt read length W71_LUNGrep2_S6_L001_R3_001.fastq.gz and W71_LUNGrep2_S6_L002_R3_001.fastq.gz should be the R2.
Comment: ID unifiying across different datasets by GenoMax 154k
Each database has their own method of annotation/validation. Depending on resources available there may be a lag between the databases in t…
Comment: low quality data or file name swapping -- cellranger arc errors when processing by Wu-Sheng Zhang ▴ 10
Hi @arup , thank you very much for your suggestions, and here are the results -- they seems correct. May I have your suggestions? Thank you…
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