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GATK SortSamSpark error: Failed to load org.broadinstitute.hellbender.Main
sortsamspark spark gatk
4.2 years ago by dragon940401 • 0
3
votes
2
replies
1.5k
views
How to activate and install bioinformatics software
Biostar-handbook
updated 2.6 years ago by 45k • written 4.2 years ago by ▴ 20
5
votes
6
replies
1.9k
views
Forum: Suggestion of Biostatistics book.
RNA-SEQ R Biostatics
updated 4.2 years ago by ★ 2.9k • written 4.2 years ago by ▴ 30
3
votes
2
replies
1.2k
views
How to know the positions of contigs in a reference genome
mapping positions alignment reference genome contigs
updated 4.2 years ago by 153k • written 4.2 years ago by ▴ 20
0
votes
0
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661
views
how can I analyse gender spesific CNV analysis with CNVkit?
diagram gender CNV CNVkit log2
4.2 years ago by enes ▴ 40
0
votes
4
replies
1.3k
views
extract the ids and key values
extract grep
updated 4.2 years ago by 9.3k • written 4.2 years ago by ▴ 80
0
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0
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887
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liftover results usage: input bed file and output bed file have different rows, how can I link coordinates between input and output files?
unmapped liftover coordinates relationship
4.2 years ago by wangjinpeng0225 ▴ 30
2
votes
3
replies
2.9k
views
cutadapt: error: unused arguments //not recognizing my sequences when using a loop?
cutadapter
4.2 years ago by Kirsten • 0
1
vote
4
replies
1.5k
views
Divide the genome to vary lengths windows in R
bedtools R BED
updated 4.2 years ago by 45k • written 4.2 years ago by ▴ 40
3
votes
4
replies
1.4k
views
plink2 cannot identify options when looping the chromosomes
plink2 plink
4.2 years ago by okiedokie1208 ▴ 40
2
votes
10
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3.0k
views
How to search for genes 100Kb up and downstream of any genomic site
R
updated 4.2 years ago by 36k • written 4.2 years ago by ▴ 50
1
vote
1
reply
722
views
How to extract genes from RNA-seq using its reference genome?
of alignment RNAseq genes list
updated 4.2 years ago by 153k • written 4.2 years ago by • 0
0
votes
0
replies
690
views
CHIPQC problem ( the wrong ReadL and no FragL RelCC)
CHIPQC
updated 4.2 years ago by 153k • written 4.2 years ago by • 0
0
votes
3
replies
3.1k
views
WGCNA: scale-free topology fit indexes are negative
gene r WGCNA
updated 4.2 years ago by 3.9k • written 4.2 years ago by ▴ 10
6
votes
8
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2.9k
views
what are the reasons to find so few Differentially expressed genes (DEGs)?
Gene RNA
updated 4.2 years ago by 15k • written 4.2 years ago by ▴ 1000
0
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0
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696
views
extract exons/introns from multiple fasta files with gene sequences
intron splicing fasta CDS exon
4.2 years ago by ramiroricardo • 0
0
votes
1
reply
2.0k
views
Plink: --keep flag
--keep subset plink
updated 4.2 years ago by 11k • written 4.2 years ago by • 0
1
vote
3
replies
1.5k
views
Error when searching for matches using the PSSM score with proteins (.motif BioPython)
protein motif python biopython
3.1 years ago by Agenor Neto ▴ 10
2
votes
2
replies
1.1k
views
Detecting RNA Editing in Single-Cell RNA-seq
scRNAseq RNAediting
4.2 years ago by fouerghi20 ▴ 90
3
votes
3
replies
1.5k
views
Intrinsically disordered region(IDR) or Intrinsically disordered Protein(IDP)
biopython
updated 4.2 years ago by 22k • written 4.2 years ago by • 0
0
votes
3
replies
3.4k
views
STARsolo --EmptyDrops_CR parameters
RNA-seq alignment STAR
updated 3.6 years ago by • 0 • written 4.2 years ago by ▴ 70
3
votes
3
replies
3.6k
views
Nanopore tutorial for beginners
nanopore
updated 2.5 years ago by 45k • written 4.2 years ago by ★ 1.3k
0
votes
0
replies
566
views
Mitochondrial targeting sequence
mts crispr geneediting gene Sequence
4.2 years ago by chiti.agarwal ▴ 10
3
votes
2
replies
3.3k
views
tools for identifying mitochondrial-targeting sequence in different proteins
alignment sequencing mtp
updated 2.9 years ago by 45k • written 10.2 years ago by ▴ 50
9
votes
6
replies
10.0k
views
6 follow
Quadruplex sequence batch prediction
Quadruplex
updated 2.6 years ago by 45k • written 10.4 years ago by ▴ 50
0
votes
0
replies
604
views
Read distribution tool accounting for read orientation
RNA
4.2 years ago by VHahaut ★ 1.2k
2
votes
1
reply
988
views
Different ab initio 3D structure prediction for same protein sequence by trRosetta
3D protein trRosetta structure prediction
updated 4.2 years ago by ▴ 390 • written 4.2 years ago by ▴ 80
0
votes
3
replies
1.4k
views
Local realignment around indels
local realignment
4.2 years ago by Elisa • 0
1
vote
5
replies
3.1k
views
How to create a proper design matrix/contrast matrix for methylation 850k analysis in limma?
850k methylation analysis R limma design matrix
updated 4.2 years ago by • 0 • written 5.6 years ago by ▴ 140
2
votes
5
replies
4.5k
views
Snakemake error: "Removing output files of failed job since they might be corrupted:"
Snakemake
updated 4.2 years ago by 15k • written 4.2 years ago by ▴ 100
2
votes
5
replies
5.3k
views
Beagle: Skip intervals with no common markers
beagle plink vcf conformgt
updated 4.2 years ago by ▴ 20 • written 5.6 years ago by ▴ 10
1
vote
0
replies
675
views
Duplicate genotypes after phasing in Beagle
Beagle Phasing
4.2 years ago by PKW ▴ 110
1
vote
0
replies
1.1k
views
Deeptools plotPCA on RNA-seq help
PCA deeptools RNAseq
4.2 years ago by jrichardalbert ▴ 10
1
vote
2
replies
1.2k
views
How to perform differential expression on proteomics data?
proteomics TMT Differential-Expression R
4.2 years ago by lenC_biotecLover ▴ 90
2
votes
6
replies
3.4k
views
How to find overlapping coordinates of a gtf file
gtf-file sequencing genome annotation RNA-Seq
updated 4.2 years ago by 36k • written 4.2 years ago by ▴ 320
0
votes
4
replies
1.6k
views
how to merge two files in two columns using bash command lines
assembly fasta trinity
updated 4.2 years ago by ▴ 410 • written 4.2 years ago by ▴ 20
0
votes
0
replies
677
views
Series Matrix File in GEO
GEO labeling GEO2R
4.2 years ago by Sonia • 0
2
votes
2
replies
1.1k
views
merging fasta sequences into a single fasta sequence in large file
fasta sequences
updated 4.2 years ago by 56k • written 4.2 years ago by ▴ 10
0
votes
0
replies
1.1k
views
Request for feature addition to p3_in.pl to extract specified length of flanking sequence around a SSR form MISA output file (genome.misa)
Primer3 ssr MISA Flanking Sequence
updated 3.7 years ago by ▴ 60 • written 4.2 years ago by • 0
6
votes
6
replies
1.7k
views
Divide by a specified member in a group in R
R dplyr
updated 4.2 years ago by ★ 2.9k • written 4.2 years ago by ▴ 700
4
votes
12
replies
2.6k
views
RNAseq analysis for aspergillus niger ?
aspergillus niger RNAseq
4.2 years ago by najibveto ▴ 130
0
votes
0
replies
571
views
Mutation rate of repeat elements
transposable mutation rate evolution elements repeat
4.2 years ago by kanamori.shunsuke • 0
0
votes
6
replies
2.2k
views
Creating Annotation GTF/GFF file
HG38 Annotation Rna-Seq Genome
updated 4.2 years ago by ★ 2.2k • written 4.2 years ago by ▴ 40
0
votes
2
replies
1.7k
views
RepeatMasker sequence identifier error
RepeatMasker
updated 4.2 years ago by ▴ 40 • written 4.2 years ago by • 0
0
votes
5
replies
1.6k
views
Create BED- or GVCF-type file for human genome
GRCh37 FASTA GVCF VCF hg19
updated 4.2 years ago by 45k • written 4.2 years ago by ▴ 250
1
vote
5
replies
2.6k
views
conform-gt error "Non-unique marker ID: ."
conform-gt error
updated 4.1 years ago by ▴ 20 • written 4.2 years ago by ▴ 20
0
votes
0
replies
673
views
map miRNA to chromosomal locations
python miRNA R location chromosome
4.2 years ago by ehruan ▴ 10
1
vote
2
replies
1.1k
views
How to calculate the difference between the RNA-Seq individual samples?
comparison expression edgeR replicates R
4.2 years ago by mohammedtoufiq91 ▴ 270
0
votes
0
replies
832
views
Job: Research assistants or postdoctoral fellows in computational biology/bioinformatics (UMass Medical School, Worcester, Massachusetts)
computational sequencing genetics genomics
updated 4.2 years ago by 45k • written 4.2 years ago by ▴ 10
1
vote
1
reply
731
views
any way to use RNA seq mapping to choose between competing gene models?
gene rnaseq prediction
updated 4.2 years ago by 153k • written 4.2 years ago by ▴ 40
121,903 results • Page 625 of 2439
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Answer: Tried building a compact sequence format with 4-bit storage
Tried building a compact sequence format with 4-bit storage
Shift in RNA 3' position, Term-Seq vs RNASeq
Comment: STARlong for pacbio Isoseq reads
Comment: Automatically annotating a feature using a genbank file
Answer: Is this PCA plot correct??
Answer: Is this PCA plot correct??
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Recent Replies
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…
Comment: RNA-SEQ where only a subset of genes is of interest by piffelpaff • 0
Sorry to revive this ancient thread but I'm currently discussing the same question with some people in my lab and would love to somebody po…
Answer: STARlong for pacbio Isoseq reads by YuZJ • 0
Hello, you may try deSALT (DOI: 10.1186/s13059-019-1895-9, GitHub: ydLiu-HIT/deSALT) or uLTRA (DOI: 10.1093/bioinformatics/btab540, GitHub:…
Comment: Shift in RNA 3' position, Term-Seq vs RNASeq by acvill ▴ 350
Without knowing the details of the Term-seq method, could the 38 nt shift be accounted for by the difference in the position of the ribosom…
Comment: STARlong for pacbio Isoseq reads by Buffo ★ 2.4k
Thanks, I'll give it a try.
Comment: STARlong for pacbio Isoseq reads by GenoMax 153k
You could give `mapPacBio.sh` from BBMap suite a try while you wait for other answers. That works for reads up to 6 kb. BBMap has a new hom…
Comment: STARlong for pacbio Isoseq reads by Buffo ★ 2.4k
The average is 1.8kb. I was planning to post it on GitHub, but it seems like the repository has been unattended for the last months, so I d…
Comment: Getting just fastqc.zip file? by GenoMax 153k
Yes, You can either use it on command line or use the graphical user interface.
Comment: STARlong for pacbio Isoseq reads by GenoMax 153k
What is the average length of your reads? That error sounds like a bug, so you may want to post that on `STAR` repo as an issue. I assume …
Comment: Getting just fastqc.zip file? by pourhangleila95 • 0
I want to perform fastQC on my data.Do you use fastQC software for doing it?
Comment: Whole Genome Sequencing IG regions by 719 • 0
Sorry for the poor wording of the original post, also should say I really appreciate people taking a moment to look at my post. My main con…
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