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538 results • Page 2 of 11
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0
votes
0
replies
104
views
Determining Cutoff for score in a bed file in ATAC-seq Data Analysis
bed ATAC-seq
updated 4 days ago by 39k • written 4 days ago by • 0
1
vote
3
replies
217
views
To call variants can I use my aligned WGS data as a reference genome
VCF samtools reference genome
updated 4 days ago by 129k • written 4 days ago by • 0
0
votes
0
replies
106
views
snpEff error. No CDS checked
snpEff gtf WES
4 days ago by fifty_fifty ▴ 40
0
votes
0
replies
105
views
Tool to align metagenomic data to reference genome
tool metagenomics alignment
4 days ago by Maddie • 0
1
vote
2
replies
204
views
how to look for interactions between different chromosomes
SNP interactions Gene HiC
3 days ago by rheab1230 ▴ 140
2
votes
4
replies
234
views
Filter VCF file for variant alleles
VCF variants bcftools vcftools
updated 4 days ago by 39k • written 4 days ago by • 0
1
vote
0
replies
106
views
Linear models with limma: coefficients not estimatable, are the others OK?
limma
4 days ago by fr ▴ 200
0
votes
2
replies
173
views
Ambient RNA expression correction
scRNAseq SoupX Seurat
updated 4 days ago by 12k • written 4 days ago by ▴ 10
0
votes
2
replies
162
views
readGenericHeader() error message Limma
rna limma microarray genomics normalization
4 days ago by survive • 0
1
vote
1
reply
127
views
mitochondrial genome, SRA PacBio sequencing.
Mitochondrial PacBio SRA Mitogenome
updated 4 days ago by 129k • written 4 days ago by ▴ 20
0
votes
0
replies
80
views
metagenomics data - AMR genes
amr resistome resistance ARG metagenomics
5 days ago by aziznasr1920 ▴ 10
1
vote
3
replies
183
views
How to get a comperative result of 2 bed files?
bam cnv bed
updated 4 days ago by 154k • written 5 days ago by • 0
0
votes
0
replies
74
views
1000G reference panel for LD clumping
LD
5 days ago by en_keser • 0
0
votes
0
replies
84
views
Nucleotide alignments from mmseqs "tblastn"
mmseqs2 tblastn mmseqs
5 days ago by saladi ▴ 30
0
votes
2
replies
608
views
ERROR running Cuffmerge in reference based RNA-SEQ analysis?
cuffmerge RNA-Seq Cufflinks
updated 5 days ago by 39k • written 13 months ago by • 0
0
votes
7
replies
564
views
How to deal with duplicated gene IDs in TCGA RNA expression data?
TCGA Expression mRNA
updated 5 days ago by ★ 2.9k • written 9 days ago by ▴ 30
0
votes
3
replies
200
views
Dada2 in Qiime2: losing reads during merging
Qiime2 Chimer Dada2
updated 4 days ago by 3.3k • written 5 days ago by ▴ 80
0
votes
1
reply
153
views
NCBI Common Taxonomy Tree
phylogenetic-tree comparative-taxonomy ncbi
updated 5 days ago by 129k • written 5 days ago by • 0
0
votes
3
replies
188
views
minimap's SAM file MAPQ value for the unique alignments
minimap MAPQ RNAseq
4 days ago by Mohd ▴ 20
1
vote
2
replies
176
views
sorting BAM file
BAM
updated 5 days ago by 72k • written 5 days ago by • 0
0
votes
0
replies
88
views
Converting rds file to h5ad and saving raw counts as X
R seurat
updated 6 days ago by 11k • written 6 days ago by ▴ 50
0
votes
1
reply
146
views
Seurat: How to get all genes name of a cell ?
seurat
updated 5 days ago by ★ 1.2k • written 6 days ago by ▴ 640
1
vote
0
replies
233
views
miRDeep2 installation showing "ln: failed to create symbolic link './randfold': File exists" error.
miRDeep2
updated 5 days ago by 39k • written 6 days ago by • 0
0
votes
0
replies
102
views
Bulk RNA sequencing time course pathway analysis progression visualization
time-course RNA-seq pathway
updated 5 days ago by 39k • written 6 days ago by • 0
2
votes
2
replies
111
views
how to use Hemtools bed2vcf?
vcf linux conversion bed
updated 6 days ago by 154k • written 6 days ago by ▴ 10
0
votes
1
reply
149
views
How to calculate SARS-2'S evolutionary rate
evolutionary-rate
updated 5 days ago by 39k • written 6 days ago by • 0
0
votes
0
replies
84
views
How to retrieve non-redundant restriction enzymes database from Rebase?
Rebase Databases enzymes Restriction
6 days ago by Mahmoud Reda ▴ 10
1
vote
2
replies
202
views
Converting RefSeq protein accession IDs into entreZ IDs
RNA-SEQ
5 days ago by Pegasus ▴ 90
0
votes
0
replies
120
views
Merging multiple PLINK files
plink merging
6 days ago by Nejla • 0
0
votes
0
replies
118
views
References selected by ExomeDepth CNV
CNV ExomeDepth
updated 6 days ago by 129k • written 6 days ago by • 0
0
votes
2
replies
223
views
BCR/TCR analysis using target capture sequencing data
capture ngs TCR BCR
5 days ago by J.F.Jiang ▴ 900
0
votes
2
replies
203
views
Upstream pseudogene causing MAPQ 0 and exclusion during variant calling
Mapping Variant-calling masking
updated 6 days ago by 39k • written 7 days ago by ▴ 130
1
vote
3
replies
702
views
Regular Expression for conversion
Linux grep
updated 5 days ago by 21k • written 19 months ago by ▴ 10
0
votes
1
reply
166
views
weird behaviour on bedtools
bedtools RNA-Seq
updated 5 days ago by 39k • written 7 days ago by ▴ 110
0
votes
2
replies
174
views
fgsea/clusterProfiler Packages for nCounter data enrichment analysis
nanostring gsea r
7 days ago by pg45863 • 0
0
votes
1
reply
139
views
ABySS Process Killed
ABySS genome assembly
updated 7 days ago by 129k • written 7 days ago by • 0
0
votes
0
replies
99
views
Cell type sub-clustering across multiple samples in scRNA-seq
scRNA-seq
7 days ago by narges.bioinf • 0
0
votes
3
replies
224
views
Query qbout single cell sequencing
fastq ScRNA
updated 5 days ago by 39k • written 7 days ago by ▴ 20
0
votes
1
reply
186
views
How to introduce normalized and scaled seurat data into monocle 3?
Monocle scRNA-seq Seurat
updated 6 days ago by ▴ 950 • written 7 days ago by • 0
0
votes
1
reply
179
views
Why coordinate sort is required in sambamba depths?
sorting coordinate sambamba linux samtools
updated 7 days ago by 154k • written 7 days ago by ▴ 10
0
votes
4
replies
284
views
I need help with a methyl array data analysis
methyl_array DMPs DMRs beta_value r
7 days ago by Ahmad ▴ 10
0
votes
2
replies
248
views
Error in download library file in expression console software
expression microarray console
5 days ago by Mohammad • 0
0
votes
6
replies
340
views
Demultiplexing bam file
demultiplexing bam_file Iontorrent
7 days ago by hasani.iut6 ▴ 60
1
vote
2
replies
264
views
DEgs RNAseq
RNAseq
7 days ago by Juan • 0
0
votes
0
replies
176
views
Different alternatives for downloading GWAS summary statistics en masse
GWAS
5 days ago by Vincent Laufer ★ 2.9k
0
votes
1
reply
243
views
problem of Global Biobank Meta-analysis Initiative
GWAS
updated 7 days ago by ★ 3.0k • written 8 days ago by • 0
1
vote
1
reply
230
views
DownsampleSam
picard DownsampleSam
updated 8 days ago by 154k • written 8 days ago by • 0
0
votes
1
reply
237
views
Error while running Megahit
Megahit
updated 8 days ago by ★ 23k • written 9 days ago by • 0
2
votes
5
replies
414
views
Cutadapt error: too many parameters.
cutadapt parallel bash
6 days ago by DanielEB_fisk • 0
0
votes
0
replies
196
views
corresponding clinical data from TCGA database of PSI values for CCA AS events in spliceseq database
TCGA
9 days ago by dima • 0
538 results • Page 2 of 11
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Answer: How To Predict Pseudogenes In A Genome
A: How To Predict Pseudogenes In A Genome
A: How To Predict Pseudogenes In A Genome
A: How To Predict Pseudogenes In A Genome
How To Predict Pseudogenes In A Genome
C: parsing fasta file
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Recent Replies
Answer: Installation of PPFinder by GenoMax 129k
Since the software is still [**listed on the Brent lab**][1] website your best bet would be to email the investigator and ask that they fix…
Comment: How to calculate TPM from featureCounts output by rpolicastro 12k
If you want to go that route, yes.
Comment: Difference between USCS exon coordinates and ensembl by ATpoint 72k
What did you download from UCSC? 1-off usually means one file is zero-based and the other 1-based. BED files from UCSC are 0-based, Ensembl…
Comment: Alignment of case vs. control from different origin by sativus • 0
Thank you kindly for the explanation, it is highly appreciated. I suppose i was a bit confused as you quite often see people validating the…
Answer: Gene enrichment analysis by nux ▴ 10
Hello. For this you have to select 'hyper' as your method and then provide a complete list of genes which both include the candidate and no…
Comment: CNNScoreVariants Error by bestone ▴ 10
Thank you for replying I updated it worked but it gives another Error A USER ERROR has occurred: Invalid argument ' -V'.
Comment: Impute haplotypes (ImputePipelinePlugin) execution error - PHG by jrodrigu • 0
Thank you so much. I made the suggested changes. However, I still have the same problem. Please check the new log file. https://github.c…
Comment: Getting same value for start and end position, "DNA methylation" by ATpoint 72k
That's a comment, not an answer, please use `ADD COMMENT`.
Comment: Getting same value for start and end position, "DNA methylation" by bioinfo_ga ▴ 50
Are you working on bisulphite kind of data or chipseq ????
Answer: How to calculate TPM from featureCounts output by bioinfo_ga ▴ 50
hi , You can use a python package rnanorm [https://pypi.org/project/rnanorm/]. The input required are your read count values from feature …
Comment: How to split a scRNA reads BAM or FASTQ file to a separate file for each cell by by biofalconch ▴ 580
Hey, if you arelady have the barcodes, you could use samtools `samtools view -h -b -f CB:Z:TAAGAGATCCTATGTT > TAAGAGATCCTATGTT.bam` Hope…
Answer: How to split a scRNA reads BAM or FASTQ file to a separate file for each cell by by biofalconch ▴ 580
Here is a code that should work, but just like everyone else in the comments I'm a little confused why would you need to separate them: …
Comment: Make a BedGraph file by kirillkirilenko ▴ 10
It works, thank you!
Comment: CNNScoreVariants Error by Pierre Lindenbaum 154k
check you have a complete environment for GATK , including the python module "keras". https://gatk.broadinstitute.org/hc/en-us/articles/360…
Comment: How to split a scRNA reads BAM or FASTQ file to a separate file for each cell by by Cathal • 0
Did you have any luck in splitting the BAM file based on the 10x cell barcode? I would like to split a BAM file based to only include 5 spe…
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