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23
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22
replies
40k
views
6 follow
Converting VCF to PLINK .bed binary fileset to check for pedigree errors with KING: How do conversion tools make the PLINK .fam file, without asking …
plink vcf fam gatk vcftools
updated 6 months ago by • 0 • written 5.1 years ago by ▴ 250
4
votes
4
replies
35k
views
How to convert a URL into a DOI programmatically
pubmed doi url
written 6.7 years ago by ▴ 100
4
votes
13
replies
27k
views
6 follow
[main_samview] fail to read the header from sample.bam
alignment
updated 11 months ago by • 0 • written 5.3 years ago by ▴ 20
20
votes
15
replies
26k
views
8 follow
Converting SNP from chr:pos to rs number using PLINK?
plink SNP
updated 10 months ago by 39k • written 7.4 years ago by ▴ 190
4
votes
6
replies
24k
views
terminate called after throwing an instance of 'std::bad_alloc?
bedtools linux data
4.1 years ago by star ▴ 340
1
vote
3
replies
24k
views
How to extract vcf.gz and vcf.gz.tbi
SNP sequence gene
updated 4.9 years ago by 154k • written 4.9 years ago by ▴ 20
3
votes
4
replies
21k
views
Using nr database for BLAST search
nr database blast blastp
updated 6.8 years ago by 20 • written 6.9 years ago by ▴ 20
9
votes
4
replies
21k
views
What is the definition of "read depth" vs "coverage"? (again...)
coverage depth read depth
6.1 years ago by ariel.balter ▴ 200
2
votes
4
replies
20k
views
Error in file(file, "rt") : cannot open the connection
R MicroRNA TXT FORMAT
updated 7.1 years ago by 129k • written 7.1 years ago by • 0
1
vote
5
replies
18k
views
Calculating the sequence similarity and percentage of matched sequences
alignment sequence
updated 5.5 years ago by • 0 • written 5.6 years ago by ▴ 10
7
votes
16
replies
18k
views
featureCounts: Low percentage of assigned fragments
RNA-Seq rna-seq
6.8 years ago by aggregatibacter ▴ 180
27
votes
17
replies
17k
views
12 follow
Dotplot for filtered pathways result
pathways ggplot2 clusterProfiler r dotplot
18 months ago by Leite ★ 1.2k
2
votes
8
replies
17k
views
Using vcfutils.pl command
alignment
updated 13 months ago by 39k • written 8.3 years ago by ▴ 40
2
votes
10
replies
16k
views
How do you use the Aspera ascp command?
aspera gigascience gigaDb
updated 21 months ago by 39k • written 7.6 years ago by ▴ 940
2
votes
3
replies
16k
views
Subsetting - Raw Counts from Seurat Object
seurat raw counts RNA-Seq
3.1 years ago by David_emir ▴ 460
16
votes
38
replies
16k
views
Differential gene Analysis by Limma
Limma Microarray R
updated 13 months ago by 39k • written 8.3 years ago by ▴ 920
2
votes
13
replies
15k
views
convert text file to fasta file
blast
updated 6.8 years ago by 12k • written 6.8 years ago by ▴ 30
6
votes
2
replies
15k
views
Pacbio Ccs Vs Subreads Explained ?
updated 9.1 years ago by 20 • written 9.6 years ago by ▴ 40
0
votes
8
replies
15k
views
find ORF in sequence python
sequence
updated 6.4 years ago by ★ 3.9k • written 6.4 years ago by ▴ 120
2
votes
2
replies
15k
views
How to calculate the insert size for Paired-end reads
SSPACE insert-size
6.9 years ago by Ric ▴ 430
4
votes
10
replies
14k
views
How to plot a multiple line graph with Mean and Std Error for following dataset?
R
updated 5.1 years ago by 129k • written 5.1 years ago by ▴ 720
5
votes
4
replies
14k
views
glmnet package lasso error
glmnet lasso multilinear regression
5.2 years ago by demoraesdiogo2017 ▴ 90
16
votes
14
replies
14k
views
Which truseq trimmomatic adapters file to use when removing truseq adapters?
adapters trimmomatic RNA-seq
4.9 years ago by salamandra ▴ 540
0
votes
3
replies
14k
views
How to choose a TPM cut-off point
RNA-Seq transcript tpm
updated 9 months ago by 39k • written 7.6 years ago by ▴ 10
2
votes
4
replies
14k
views
TRIMMOMATRIC Nextera trimming
next-gen
updated 7 months ago by 39k • written 7.8 years ago by ▴ 10
0
votes
3
replies
14k
views
Error in (function (classes, fdef, mtable): unable to find an inherited method for function ‘annotation’ for signature ‘"character
inSilicoMerging
9.0 years ago by ira_grich • 0
3
votes
1
reply
14k
views
How do you normalize Transcript per Million TPM to compare between samples ?
RNA-Seq TPM STAR salmon quantification
6.4 years ago by ZheFrench ▴ 500
1
vote
8
replies
14k
views
HTSeq-count high number of no_feature
htseq-count rna-seq
updated 13 months ago by 39k • written 8.3 years ago by ▴ 80
7
votes
4
replies
13k
views
Use of if-else statement in snakemake rule
snakemake if-else python
updated 3.5 years ago by • 0 • written 5.9 years ago by ▴ 130
9
votes
13
replies
13k
views
GC Content of Fasta file --- Python Help
sequence
6.3 years ago by Patrick Brennan ▴ 50
1
vote
5
replies
13k
views
pheatmap: how to use legend information as row annotation?
R pheatmap legend annotation
5.2 years ago by n85825 • 0
13
votes
13
replies
13k
views
How to interpret Per sequence GC content module in FastQC for RNA-seq data?
RNA-Seq FastQC QC GC-content
3.8 years ago by Arindam Ghosh ▴ 500
8
votes
5
replies
13k
views
The comparison between HISAT2 and Tophat2
RNA-Seq Tophat2 HISAT2
updated 4.7 years ago by 39k • written 7.3 years ago by ▴ 50
3
votes
8
replies
13k
views
Error when running pheatmap
pheatmap Error in hclust
4.2 years ago by luzglongoria ▴ 40
0
votes
2
replies
13k
views
Error in -delete: invalid argument to unary operator
RNA-Seq R
3.3 years ago by ovariohisterectomia ▴ 40
6
votes
13
replies
13k
views
Fastq file is truncated error message
RNA-Seq error fastq
7.0 years ago by rob.costa1234 ▴ 310
4
votes
1
reply
13k
views
Converting BigBed to Bed format
Installing BigFile Support
8.0 years ago by sumaira.zaman10 ▴ 20
0
votes
2
replies
13k
views
How to download pfam database
sequence
updated 6.4 years ago by 9.6k • written 6.4 years ago by ▴ 30
6
votes
13
replies
12k
views
Showing FDR and log2FC in Volcano plot using R
R RNA-Seq volcano plot
updated 4.0 years ago by 11k • written 5.5 years ago by ★ 3.4k
4
votes
18
replies
12k
views
Alignment with BWA and SAMtools
BWA SAM-file SAMtools
updated 2.6 years ago by 20 • written 4.8 years ago by ▴ 30
9
votes
13
replies
12k
views
Sort bam file by coordinates using samtools
sequencing next-gen gene rna-seq Tool
updated 4.7 years ago by 16k • written 4.7 years ago by ▴ 30
0
votes
4
replies
12k
views
Unable to install XLconnect package in R studio version 3.2.1
R
updated 8 months ago by 39k • written 7.8 years ago by ▴ 10
3
votes
11
replies
12k
views
What is the acceptable % of reads that map to no feature (in RNASeq)?
htseq RNA-Seq STAR
updated 13 months ago by 39k • written 8.4 years ago by ▴ 120
2
votes
4
replies
12k
views
Run BLAST on Linux terminal
ncbi nBLAST linux blast
updated 9 months ago by 39k • written 7.7 years ago by ★ 1.2k
1
vote
2
replies
12k
views
kart file in prefetch
rna-seq
updated 6.6 years ago by 20 • written 6.8 years ago by ▴ 20
0
votes
3
replies
12k
views
How to change/remove name of annotation ComplexHeatmap package?
ComplexHeatmap R RNA-Seq annotations
updated 3.0 years ago by 39k • written 3.0 years ago by ▴ 130
0
votes
1
reply
12k
views
PLINK 1.9 - Converting PED/MAP to BED/BIM/FAM with missing values
plink
updated 6.9 years ago by 20 • written 6.9 years ago by ▴ 90
0
votes
2
replies
12k
views
GSEA error - After pruning, none of the gene sets passed size thresholds
RNA-Seq GSEA gene genome
updated 3.8 years ago by ▴ 330 • written 3.8 years ago by • 0
4
votes
12
replies
11k
views
STAR alignment error- Segmentation fault (core dumped)
alignment software error RNA-Seq STAR
4.9 years ago by EagleEye 7.5k
2
votes
1
reply
11k
views
Rename Idents in Seurat Object
RNA-Seq
3.1 years ago by Thorerges ▴ 10
1,000 results • Page 1 of 20
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Answer: I need help with a blast command, please help
Answer: I need help with a blast command, please help
Answer: NCBI API, Perl
Get a list of genes associated with a drug in 1 min
Answer: Getting species names and taxa id from assembly accession number
Pseudogenes-Can we use them?
Comment: If RNA-seq includes miRNA genes then why are there miRNA specific pipelines?
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Recent Replies
Comment: I need help with a blast command, please help by neto.pvp • 0
Thank you very much!! I'm new to this subject and I believe your answer gave me a great idea of where to go next, thanks again!!
Answer: NCBI API, Perl by GenoMax 129k
You are likely best served by using `NCBI datasets` ([**LINK**][1]) or `EntrezDirect` ([**LINK**][2]) command line tools. If you want to …
Comment: Obtain a --gene-trans-map file after rnaSPAdes by GenoMax 129k
You could try to create one: https://groups.google.com/g/trinityrnaseq-users/c/qPbWnLl4iY0 While this is from an unrelated software the so…
Comment: CNNScoreVariants Error by Pierre Lindenbaum 154k
that is another question
Comment: Difference between USCS exon coordinates and ensembl by amy__ ▴ 50
Hi @atpoint, I went to http://genome.ucsc.edu/cgi-bin/hgTables and did: 1. ![enter image description here][1] then: 2. ![enter image…
Comment: should non-protein-coding rna(e.g. lncRNA) be removed in RNA-Seq differential ex by Kermit ▴ 80
See also: https://www.biostars.org/p/9535550/#9536086
Answer: Getting species names and taxa id from assembly accession number by MirianT_NCBI ▴ 590
Hi, As an alternative, you could use [NCBI Datasets][1] for this task. NCBI Datasets allows users to retrieve metadata reports in JSON or…
Comment: Optimum setting for local blastp for ~10K sequences by sodiumnitrate ▴ 20
Thank you for the info! It turned out that running all 10k at once is actually faster than running one or two at a time!
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…
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