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1,000 results • Page 2 of 20
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0
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0
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65
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1000G reference panel for LD clumping
LD
2 days ago by en_keser • 0
0
votes
0
replies
78
views
Nucleotide alignments from mmseqs "tblastn"
mmseqs2 tblastn mmseqs
3 days ago by saladi ▴ 30
0
votes
2
replies
600
views
ERROR running Cuffmerge in reference based RNA-SEQ analysis?
cuffmerge RNA-Seq Cufflinks
updated 3 days ago by 39k • written 12 months ago by • 0
0
votes
7
replies
549
views
How to deal with duplicated gene IDs in TCGA RNA expression data?
TCGA Expression mRNA
updated 2 days ago by ★ 2.9k • written 6 days ago by ▴ 30
0
votes
3
replies
187
views
Dada2 in Qiime2: losing reads during merging
Qiime2 Chimer Dada2
updated 2 days ago by 3.3k • written 3 days ago by ▴ 80
0
votes
1
reply
147
views
NCBI Common Taxonomy Tree
phylogenetic-tree comparative-taxonomy ncbi
updated 3 days ago by 129k • written 3 days ago by • 0
0
votes
3
replies
175
views
minimap's SAM file MAPQ value for the unique alignments
minimap MAPQ RNAseq
1 day ago by Mohd ▴ 20
1
vote
2
replies
158
views
sorting BAM file
BAM
updated 2 days ago by 72k • written 3 days ago by • 0
1
vote
0
replies
88
views
Resequencing data of pangenome
NGS PanGenome Resequence
updated 3 days ago by 39k • written 3 days ago by ▴ 10
0
votes
0
replies
82
views
Converting rds file to h5ad and saving raw counts as X
R seurat
updated 3 days ago by 11k • written 3 days ago by ▴ 50
0
votes
1
reply
143
views
Seurat: How to get all genes name of a cell ?
seurat
updated 3 days ago by ★ 1.2k • written 3 days ago by ▴ 640
1
vote
0
replies
223
views
miRDeep2 installation showing "ln: failed to create symbolic link './randfold': File exists" error.
miRDeep2
updated 3 days ago by 39k • written 3 days ago by • 0
0
votes
0
replies
100
views
Bulk RNA sequencing time course pathway analysis progression visualization
time-course RNA-seq pathway
updated 3 days ago by 39k • written 3 days ago by • 0
0
votes
1
reply
142
views
How to calculate SARS-2'S evolutionary rate
evolutionary-rate
updated 3 days ago by 39k • written 3 days ago by • 0
0
votes
0
replies
81
views
How to retrieve non-redundant restriction enzymes database from Rebase?
Rebase Databases enzymes Restriction
3 days ago by Mahmoud Reda ▴ 10
1
vote
2
replies
195
views
Converting RefSeq protein accession IDs into entreZ IDs
RNA-SEQ
2 days ago by Pegasus ▴ 90
0
votes
0
replies
114
views
Merging multiple PLINK files
plink merging
4 days ago by Nejla • 0
0
votes
0
replies
114
views
References selected by ExomeDepth CNV
CNV ExomeDepth
updated 4 days ago by 129k • written 4 days ago by • 0
0
votes
2
replies
215
views
BCR/TCR analysis using target capture sequencing data
capture ngs TCR BCR
2 days ago by J.F.Jiang ▴ 900
0
votes
2
replies
195
views
Upstream pseudogene causing MAPQ 0 and exclusion during variant calling
Mapping Variant-calling masking
updated 4 days ago by 39k • written 4 days ago by ▴ 130
1
vote
3
replies
698
views
Regular Expression for conversion
Linux grep
updated 3 days ago by 21k • written 19 months ago by ▴ 10
0
votes
1
reply
160
views
weird behaviour on bedtools
bedtools RNA-Seq
updated 3 days ago by 39k • written 4 days ago by ▴ 110
0
votes
2
replies
169
views
fgsea/clusterProfiler Packages for nCounter data enrichment analysis
nanostring gsea r
4 days ago by pg45863 • 0
0
votes
1
reply
135
views
ABySS Process Killed
ABySS genome assembly
updated 4 days ago by 129k • written 4 days ago by • 0
0
votes
0
replies
95
views
Cell type sub-clustering across multiple samples in scRNA-seq
scRNA-seq
4 days ago by narges.bioinf • 0
0
votes
3
replies
221
views
Query qbout single cell sequencing
fastq ScRNA
updated 3 days ago by 39k • written 4 days ago by ▴ 20
0
votes
1
reply
172
views
How to introduce normalized and scaled seurat data into monocle 3?
Monocle scRNA-seq Seurat
updated 3 days ago by ▴ 950 • written 5 days ago by • 0
0
votes
1
reply
172
views
Why coordinate sort is required in sambamba depths?
sorting coordinate sambamba linux samtools
updated 5 days ago by 154k • written 5 days ago by ▴ 10
0
votes
4
replies
276
views
I need help with a methyl array data analysis
methyl_array DMPs DMRs beta_value r
5 days ago by Ahmad ▴ 10
0
votes
2
replies
242
views
Error in download library file in expression console software
expression microarray console
3 days ago by Mohammad • 0
0
votes
6
replies
335
views
Demultiplexing bam file
demultiplexing bam_file Iontorrent
4 days ago by hasani.iut6 ▴ 60
1
vote
2
replies
254
views
DEgs RNAseq
RNAseq
5 days ago by Juan • 0
0
votes
0
replies
165
views
Different alternatives for downloading GWAS summary statistics en masse
GWAS
3 days ago by Vincent Laufer ★ 2.9k
0
votes
1
reply
238
views
problem of Global Biobank Meta-analysis Initiative
GWAS
updated 5 days ago by ★ 3.0k • written 6 days ago by • 0
1
vote
1
reply
226
views
DownsampleSam
picard DownsampleSam
updated 6 days ago by 154k • written 6 days ago by • 0
0
votes
1
reply
230
views
Error while running Megahit
Megahit
updated 5 days ago by ★ 23k • written 6 days ago by • 0
2
votes
5
replies
403
views
Cutadapt error: too many parameters.
cutadapt parallel bash
3 days ago by DanielEB_fisk • 0
0
votes
0
replies
193
views
corresponding clinical data from TCGA database of PSI values for CCA AS events in spliceseq database
TCGA
7 days ago by dima • 0
1
vote
0
replies
251
views
How to assess which cell population is most affected by treatmant in single cell rna seq data?
transcriptomics single-cell RNA DEG
7 days ago by abbas89 ▴ 10
0
votes
1
reply
753
views
Can I send my PyMol results to a web-page as a result for a submitted query? If not, how can I get a 3d render of a protein as a result for a user su…
protein-structure pymol protein pdb python
updated 3 days ago by 21k • written 7 days ago by • 0
0
votes
1
reply
299
views
Deferentially expressed gene with high log2foldchange by DESeq2; but not meaningful at the individual level
DESeq2 RNA-seq DGEA
updated 7 days ago by ★ 2.9k • written 7 days ago by ▴ 10
1
vote
2
replies
264
views
Abyss taking a Long time to run
abyss assembly genome fastq
7 days ago by Maliha ▴ 20
0
votes
2
replies
280
views
Import or read Snapgene .dna files into R
R .dna snapgene
7 days ago by eggrandio ▴ 40
4
votes
4
replies
343
views
Segmentation fault Biopython pairwise alignment
biopython alignment
updated 3 days ago by 21k • written 7 days ago by ▴ 20
0
votes
0
replies
157
views
BEAST Divergence time Analysis
time BEAST BEAUti divergence
7 days ago by ahmadjoyyia ▴ 10
0
votes
0
replies
173
views
Differential Gene Expression analysis in heterogeneous tissues
RNA-seq deseq2
updated 7 days ago by 39k • written 7 days ago by ▴ 70
1
vote
1
reply
228
views
Variant Annotation
Variant-Annotation VCF R
updated 7 days ago by 39k • written 7 days ago by • 0
0
votes
1
reply
250
views
too many zeros in 16S rRNA amplicon sequencing data
16S rRNA
updated 6 days ago by 3.3k • written 7 days ago by ▴ 180
0
votes
1
reply
206
views
Finding Kinetic Parameters from Western Blot images
image-processing western-blot
updated 7 days ago by 39k • written 7 days ago by • 0
0
votes
0
replies
161
views
Chipseq data peak calling issue
ChIP-seq RNA sequencing
updated 3 days ago by 39k • written 7 days ago by • 0
1,000 results • Page 2 of 20
Recent Votes
Efficiently extract alignments with NH:i:1 field
Help with Samtools flags to get only primary, unique, non duplicate aligned reads
Answer: What does canonical transcript mean in the context of VEP
Answer: What does canonical transcript mean in the context of VEP
Comment: Optimum setting for local blastp for ~10K sequences
Perl. How to extract gene entry, CDS and gene sequence from a specified range from GenBank files?
Comment: How to sort gff3 according to chromosome order?
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Popular Question to carlopecoraro2 ★ 2.3k
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Recent Replies
Comment: Help with running ATAC using Encode pipeline by Chris ▴ 100
Thank you for the instruction! I see the beside json file we also have input file which I am confused. Because we have already defined the …
Comment: Comparing loci across catalogs by rycro_c • 0
Hi @Austin, Did you ever figure this out?
Comment: Low mapping percentage by Dave Carlson ★ 1.3k
I've been faced with similar issues in the past. Both option 1 and 2 seem useful. You can also treat your data as accidental metagenomic …
Comment: How to sort gff3 according to chromosome order? by Pierre Lindenbaum 154k
-s, --stable stabilize sort by disabling last-resort comparison
Comment: Low mapping percentage by GenoMax 129k
If you do have contamination (either from rRNA of same species or from true contaminant(s)) there is not much you can do about that at this…
Comment: Optimum setting for local blastp for ~10K sequences by GenoMax 129k
> Running the same sequence on the blast web server took 10 seconds Don't try to compare anything local with NCBI's web blast infrastruct…
Comment: how to Construct a Newick tree file from five large fasta files by Joe 21k
Yes, I know - but that doesn't answer the question. **What *kind* of phylogenetic tree?**
Comment: Optimum setting for local blastp for ~10K sequences by sodiumnitrate ▴ 20
Thank you for the explanation! I managed to get diamond to work, but I'm having trouble getting it to run faster than blast. For a single t…
Comment: What is "pident" (percentage of identical matches) in the "Diamond" protein alig by GenoMax 129k
That is the question @Vincent answer poses since it seems to correspond to something different. You can also create an issue on https://gi…
Answer: How to sort gff3 according to chromosome order? by GenoMax 129k
Please use `AGAT`: https://agat.readthedocs.io/en/latest/topological-sorting-of-gff-features.html
Comment: convert data frame with character column to data frame with integer column by atemedorri137798 • 0
dear @Basti : As you said in order to clarify my issue I edit question box with give an example. I will be grateful if you take a look at …
Comment: How to sort gff3 according to chromosome order? by Ram 39k
Those are your options with the `sort` utility - you can either keep the existing order or re-order by coordinate. If you're looking for a …
Comment: How to sort gff3 according to chromosome order? by BioinfoBee • 0
using sort -k1,1 doesn't keep the order of child features of each gene in output.
Comment: How to sort gff3 according to chromosome order? by Ram 39k
You're sorting by chromosome AND co-ordinates. Try just `sort -k1,1`
Comment: How to sort gff3 according to chromosome order? by BioinfoBee • 0
it does sort but not able to keep the child features (mRNA, CDS, exon) in proper order. For example, I can sort using: sort -k1,1 -k4,4n -k…
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