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Job: PhD student in precision cancer bioinformatics | Charite, Berlin, Germany
cancer berlin precision-cancer ngs
updated 2.2 years ago by 45k • written 4.5 years ago by • 0
1
vote
3
replies
1.3k
views
How do I perform MAF analysis for each family separately in PLINK?
plink family population split MAF
4.5 years ago by Alana.selli • 0
6
votes
10
replies
1.6k
views
Power of differential expression for a single gene analysis
RNA-Seq
4.5 years ago by German.M.Demidov ★ 3.0k
0
votes
0
replies
750
views
How to calculate expected heterozygosity(he) by MSA
gene software error miceosatellite MSA
updated 4.5 years ago by 20 • written 4.6 years ago by • 0
2
votes
3
replies
1.3k
views
RNASeq alignment visualisation
alignment RNA-Seq Assembly
4.5 years ago by daewowo ▴ 80
1
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1
reply
1.2k
views
Could adaptor contamination and primer dimers lead to low number of cells detected during a single cell RNA sequencing ?
RNA-Seq rna-seq alignment sequencing next-gen
updated 4.5 years ago by 153k • written 4.5 years ago by ▴ 10
0
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2
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1.4k
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How to generate dotplot using the lastz output file
R alignment
updated 2.3 years ago by 45k • written 4.5 years ago by • 0
0
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0
replies
898
views
News: Introduction to Deep Learning
Machine-Learning Deep-Learning Python
updated 2.6 years ago by 45k • written 4.5 years ago by ★ 2.6k
0
votes
3
replies
1.6k
views
prefetch and fast-dump problems?
prefetch SRA fastq-dump
updated 2.5 years ago by 45k • written 4.6 years ago by ▴ 270
2
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5
replies
1.8k
views
Select and keep only some results from DESEq2
RNA-Seq DESEq2 results R
4.5 years ago by luzglongoria ▴ 50
0
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0
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1.2k
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Error while using blastdb_aliastool - Some referenced files may be missing
blast localblast blastdb_aliastool
4.5 years ago by Sai • 0
0
votes
0
replies
408
views
Construct consensus from SE mRNA dataset
RNA-Seq Assembly
4.5 years ago by Emma • 0
17
votes
16
replies
24k
views
9 follow
Ensembl ID to ENTREZ best converter
gene
updated 9 months ago by 3.4k • written 5.3 years ago by ▴ 370
8
votes
8
replies
8.7k
views
Differential protein/biomarker expression using limma: is that possible?
RNA-Seq NPX LIMMA PROTEOMICS microarray
updated 4.3 years ago by ▴ 40 • written 4.5 years ago by ▴ 130
0
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3
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821
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Not getting the same results with biopython and NCBI
biopython
4.5 years ago by Harper • 0
0
votes
0
replies
522
views
Are TSL flag reliable for lncRNA annotation?
genome gene
4.5 years ago by imli_lkr • 0
0
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1
reply
1.3k
views
Accessing tar File Data from cBioPortal
RNA-Seq
updated 4.5 years ago by 20 • written 4.6 years ago by ▴ 50
0
votes
1
reply
1.1k
views
Help me solve this error in bigSCale2
bigSCale2 scRNAseq
updated 4.5 years ago by 5.9k • written 4.5 years ago by • 0
0
votes
0
replies
1.2k
views
Unable to convert from cram to bam
SNP software error sequencing next-gen
4.5 years ago by vinayjrao ▴ 260
0
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0
replies
693
views
Strange gstacks warning
stacks gstacks
4.5 years ago by mcrepeau ▴ 20
0
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1
reply
956
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What is each sample?
scRNA-seq
4.5 years ago by pomodoro_sinensis ▴ 130
4
votes
1
reply
1.4k
views
Reference Genome from NCBI BioProject ID or SRA
genome sequencing alignment software error
updated 4.5 years ago by 153k • written 4.5 years ago by ▴ 30
3
votes
7
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1.9k
views
[R, ShortRead] Subscript contains out-of-bounds indices
R
updated 4.5 years ago by 13k • written 4.5 years ago by ▴ 10
0
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0
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700
views
Any tool to mask specific probe sequence in an alignment bam file
bam masking probe
4.5 years ago by Ken ▴ 10
0
votes
0
replies
794
views
Issue with RGI heatmap
software error
updated 4.5 years ago by 20 • written 4.6 years ago by • 0
0
votes
3
replies
975
views
Error occured in designing a matrix
R
updated 4.5 years ago by 13k • written 4.5 years ago by ▴ 30
0
votes
0
replies
634
views
mutation analysis, top mutations, maftools
gene
4.5 years ago by Rob ▴ 180
0
votes
11
replies
2.9k
views
Bowtie2: Mate file error & internal exception
alignment next-gen sequence
updated 4.5 years ago by 153k • written 4.5 years ago by • 0
3
votes
8
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2.5k
views
Running snakemake on chromosomes in parallel
snakemake python vcf
updated 4.5 years ago by 166k • written 4.5 years ago by ▴ 10
0
votes
1
reply
794
views
Inter-tissue coexpression network analysis
correlation bipartite clustring coexpression
4.5 years ago by adR ▴ 130
1
vote
1
reply
4.2k
views
S4 Object data extraction in R
R S4
updated 4.5 years ago by 13k • written 4.5 years ago by • 0
0
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2
replies
4.3k
views
vcftool negative relatedness values for family members
vcftools kinship qc pedigree
updated 4.5 years ago by 20 • written 9.3 years ago by ▴ 10
0
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1
reply
1.5k
views
Segmentation fault with HOMER
homer HiC
updated 3.7 years ago by • 0 • written 4.5 years ago by ★ 1.5k
0
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0
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772
views
A database of cancer super-enhancers
ChIP-Seq super-enhancers cancer
4.5 years ago by MoHallal • 0
2
votes
3
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4.1k
views
BCL2FASTQ Dual-Index Barcode Collisions - Is the i5 Index not considered when determining the number of mismatches?
bcl2fastq barcode collision barcode-mismatches
updated 4.5 years ago by 153k • written 4.5 years ago by ▴ 110
2
votes
10
replies
4.3k
views
Converting an Rdata set to an excel sheet
R Gene
updated 4.5 years ago by 13k • written 4.5 years ago by • 0
0
votes
0
replies
978
views
whole length hg38 genomic repeat annotation file
RNA-Seq
4.5 years ago by dew ▴ 10
1
vote
1
reply
1.9k
views
Colour tip labels in a tree based on wildcard/expression using ggtree
ggtree colour R phylogeny dendrogram
updated 4.5 years ago by 45k • written 4.5 years ago by ▴ 30
0
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0
replies
632
views
Masses in topology files for coarse-grained molecular dynamics simulations
molecular dynamics topology simulation lipid
4.5 years ago by ballaneypranav • 0
2
votes
3
replies
2.1k
views
Renaming Fasta ID's according to their number and on specific string length
sequence
updated 4.5 years ago by 45k • written 8.6 years ago by • 0
4
votes
12
replies
2.3k
views
Dot-plot in R with different data sets.
R
updated 4.5 years ago by 13k • written 4.5 years ago by ▴ 90
5
votes
11
replies
2.7k
views
FASTQ File Comparison
sequencing genome
4.5 years ago by biohacker_tobe ▴ 80
0
votes
2
replies
882
views
Is mutation activating or inactivating?
mutation activating inactivating
updated 4.5 years ago by ▴ 300 • written 4.5 years ago by • 0
1
vote
1
reply
2.1k
views
VEP missing refseq annotation in refseq cache?
vep
updated 4.5 years ago by 24k • written 4.5 years ago by • 0
0
votes
2
replies
1.0k
views
Option -qcovs for tblastn
tblastn -qcovs blast option
4.5 years ago by melanie.m • 0
0
votes
1
reply
1.1k
views
Job: Bioinformatician to analyse clinical datasets - Faculty of Medical Sciences | Newcastle University, UK
variant-detection genomic-medicine
updated 2.2 years ago by 45k • written 4.5 years ago by • 0
0
votes
0
replies
478
views
WGCNA coexpression of deisased related module
R
4.5 years ago by mahmudaga • 0
0
votes
4
replies
1.3k
views
STAR alignment loop segmentation fualt (core dumped)
STAR
updated 2.3 years ago by 45k • written 4.6 years ago by • 0
0
votes
0
replies
616
views
Normalization step and use of package in differential junction expression analysis
RNA-Seq as junction-usage RJunBase ASJA
4.5 years ago by Elvira Nightingale • 0
2
votes
3
replies
7.5k
views
How to get fastq files of SRA in Galaxy
RNA-Seq next-gen sequencing
updated 4.5 years ago by ▴ 130 • written 4.5 years ago by ▴ 10
121,910 results • Page 694 of 2439
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Tried building a compact sequence format with 4-bit storage
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Recent Replies
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…
Answer: Tried building a compact sequence format with 4-bit storage by Matthias Zepper 5.1k
Hello Pranava, Thanks for sharing your repository. Devising a new file format is an interesting undertaking and certainly a task with many…
Answer: Gene Ontology Enrichment with LOC gene IDs in Common Carp (Cyprinus carpio) by GenoMax 153k
`LOC` gene ID's are often assigned to uncharacterized genes and you may not get useful information from databases for them, thus they will …
Comment: Whole Genome Sequencing IG regions by GenoMax 153k
> are the calls I am seeing reliable or should I take them with something of a pinch of salt? Not sure what calls you are referring to but…
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