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Filtering for tag: next-gen • reset
1
vote
1
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342
views
Calling TE sequences from VCF files
next-gen sniffles variant_calling
updated 8 days ago by • 0 • written 16 months ago by ▴ 80
1
vote
2
replies
299
views
Why is mapper.pl from mirdeep2 producing an empty mapping file?
mirna ngs next-gen
updated 9 days ago by ▴ 10 • written 4 months ago by ▴ 250
3
votes
3
replies
329
views
Downsampling fastq reads
next-gen metagenomics
updated 14 days ago by ▴ 280 • written 9 weeks ago by • 0
1
vote
2
replies
102
views
Want to know whether this p-adj value is acceptable
RNA-Seq next-gen sequencing
updated 23 days ago by 47k • written 23 days ago by • 0
0
votes
6
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168
views
IDT xGen Exome Research Panel v2 vs Twist Human exome core
next-gen genome sequence
updated 22 days ago by ★ 2.0k • written 23 days ago by • 0
0
votes
1
reply
116
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Cheat Sheet for NGS data analysis
next-gen cheat-sheet guidebook pdf NGS
23 days ago by angsudas62 • 0
0
votes
0
replies
179
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Looking to annotate concatenated VCF files on Galaxy for Hg19 reference genome. Need setup guidance.
genome next-gen sequencing sequence gene
updated 24 days ago by 20 • written 9 weeks ago by ▴ 20
0
votes
0
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127
views
Homer annotatePeaks.pl motif density histogram output only showing 0s for motif occurrences
ATAC-seq Homer next-gen ChIP-Seq motif
24 days ago by rintsen.sherpa • 0
3
votes
4
replies
208
views
Split VCF into separate VCFs by SNP count
vcf bcftools next-gen
19 days ago by timothy.delory ▴ 20
5
votes
3
replies
125
views
How to download RNA files in the easiest way? (from NCBI's SRA)
RNA-Seq rna-seq next-gen sequencing genome
25 days ago by GoldenRetriever ▴ 40
3
votes
5
replies
113
views
PLINK:Error: Variant '.' is not biallelic. To obtain a full list of merge failures
SNP Assembly genome next-gen
26 days ago by williamsbrian5064 ▴ 380
0
votes
1
reply
90
views
How can I convert mouse microarray's Probe IDs into gene names?
R next-gen gene
26 days ago by moutazhatem.mh • 0
3
votes
3
replies
385
views
Help regarding RNAseq data analysis.
RNA-Seq alignment next-gen
updated 26 days ago by 20 • written 21 months ago by • 0
8
votes
10
replies
217
views
Performing Differential expression analysis using DESeq with 3 conditions
RNA-Seq Deseq2 R next-gen bioconductor
26 days ago by bionewbie • 0
5
votes
8
replies
169
views
A layman trying to understand what a FASTA file is
RNA-Seq sequencing next-gen gene tutorial
updated 27 days ago by 47k • written 27 days ago by ▴ 40
1
vote
2
replies
97
views
In-silico downsizing to estimate the DNA input
sequencing snp next-gen
updated 27 days ago by 9.7k • written 27 days ago by ▴ 30
0
votes
0
replies
91
views
Run TSS predator without TEX wig libraries
RNA-Seq sequencing next-gen software error
27 days ago by qstefano ▴ 20
0
votes
2
replies
112
views
How to perform Linkage Disequilibrium analysis for significantly associated K-mers?
next-gen genome snp assembly
updated 27 days ago by • 0 • written 29 days ago by ▴ 40
0
votes
0
replies
136
views
Is it possible to call variants using cram files?
next-gen sequencing SNP
27 days ago by vinayjrao ▴ 200
0
votes
2
replies
118
views
How much sequencing coverage do you need in order to detect SNP's across the whole genome
sequencing SNP ChIP-Seq next-gen
28 days ago by dk0319 ▴ 20
0
votes
1
reply
89
views
Is there a straightforward way to use RNA alignment with the genome to infer exon-intron structure?
RNA-Seq genome alignment sequencing next-gen
28 days ago by charleslindberg976 • 0
143
votes
34
replies
49k
views
31 follow
Tutorial: Tools For Metagenomic Data Analysis
metagenomics next-gen tutorial Tutorial
updated 28 days ago by ▴ 110 • written 8.4 years ago by ★ 1.6k
1
vote
1
reply
175
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 28 days ago by 99k • written 28 days ago by • 0
0
votes
0
replies
108
views
Unable to convert from cram to bam
SNP software error sequencing next-gen
28 days ago by vinayjrao ▴ 200
0
votes
11
replies
148
views
Bowtie2: Mate file error & internal exception
alignment next-gen sequence
updated 28 days ago by 99k • written 28 days ago by • 0
0
votes
3
replies
137
views
How to get fastq files of SRA in Galaxy
RNA-Seq next-gen sequencing
updated 29 days ago by ▴ 20 • written 29 days ago by • 0
1
vote
0
replies
179
views
Job: Postdoc Fellowships - EMBL | Stanford Life Science Alliance
rna-seq genome sequencing next-gen gene Job
29 days ago by stanford ▴ 10
0
votes
0
replies
180
views
Is it possible to do an analysis of rna-seq of specific data from dataset or should I do the whole dataset?
RNA-Seq sequence next-gen
4 weeks ago by ashwing.kofficial • 0
1
vote
3
replies
108
views
What file to use for Deseq2 and where to get it from
RNA-Seq sequencing next-gen
updated 4 weeks ago by 47k • written 4 weeks ago by • 0
0
votes
0
replies
105
views
Why do my polysome and monosome-RNAs map to less exons?
RNA-Seq sequencing alignment next-gen Assembly
4 weeks ago by joetaylor268 ▴ 20
0
votes
0
replies
181
views
Job: Senior Bioinformatics Scientist at Boston Children's Hospital
RNA-Seq next-gen scRNA-seq bioinformatics Job
4 weeks ago by shira.rockowitz ▴ 10
0
votes
0
replies
125
views
Job: Postdoctoral Research Fellow position in neurodevelopmental genetics research
genome next-gen R Job
4 weeks ago by ryan.yuen • 0
0
votes
0
replies
128
views
Mutect2 failing to produce F1R2.tar.gz and stat files on TCGA bams (tumor-normal pairs)
next-gen mutect2
updated 4 weeks ago by 99k • written 4 weeks ago by • 0
1
vote
0
replies
97
views
Single-cell-ATAC normalization and merginig
next-gen R sequencing
4 weeks ago by C4 ▴ 10
0
votes
1
reply
81
views
How will the fusion sequence looks like in RNA level
rna-seq next-gen
4 weeks ago by sichen0415 • 0
1
vote
5
replies
159
views
GO Terms - most common between - many gene lists (from 36 scRNAseq clusters)
RNA-Seq next-gen
4 weeks ago by kieran.short • 0
0
votes
2
replies
126
views
Data Comparison in python
sequencing next-gen sequence snp gene
updated 4 weeks ago by ★ 10k • written 4 weeks ago by • 0
6
votes
6
replies
125
views
Sequencing lane and introduction of batch variation
RNA-Seq sequencing next-gen genome
4 weeks ago by joetaylor268 ▴ 20
0
votes
3
replies
241
views
Must an experimentally proven disease-relevant gene appear significantly differentially expressed on RNA sequencing analysis?
RNA-Seq rna-seq R next-gen
4 weeks ago by charlesgwellem • 0
1
vote
2
replies
2.1k
views
Filter field are all ".", no "PASS" in vcf file ?
software error next-gen sequencing genome
updated 4 weeks ago by • 0 • written 6.6 years ago by ▴ 100
5
votes
2
replies
125
views
Split Multimer Sequences at motif in FASTQ
sequencing next-gen fastq split motif
updated 5 weeks ago by 99k • written 5 weeks ago by ▴ 10
2
votes
3
replies
196
views
Basecalling of Nanopore Raw file
sequencing next-gen genome
10 days ago by Abhisek • 0
0
votes
2
replies
108
views
Fatal error in galaxy program
RNA-Seq next-gen sequence
5 weeks ago by ashwing.kofficial • 0
13
votes
7
replies
132
views
Remove uncharacterized chromosomes from reference fasta file
Assembly genome sequence next-gen
updated 5 weeks ago by 5.1k • written 5 weeks ago by ▴ 380
4
votes
7
replies
114
views
How do I install Boost and the bjam build engine for Cufflinks
RNA-Seq rna-seq next-gen
5 weeks ago by giusdalt95 • 0
0
votes
0
replies
142
views
Can we get information regarding microRNA expression from small RNA-seq ?
RNA-Seq next-gen
updated 5 weeks ago by 47k • written 5 weeks ago by • 0
0
votes
1
reply
200
views
What is the diffecence between SMART-seq2 & Smart-seq2 protocol in single cell analysis?
RNA-Seq rna-seq sequencing next-gen
5 weeks ago by atulchandrasingha • 0
0
votes
1
reply
146
views
Genome sequence upload from NCBI in galaxy for RNA-seq data analysis
RNA-Seq next-gen alignment genome
5 weeks ago by abhisekdey061 • 0
3
votes
4
replies
104
views
Extracting sequencing data from SRA accesion
rna-seq next-gen sequence
updated 5 weeks ago by ▴ 10 • written 5 weeks ago by • 0
0
votes
0
replies
94
views
Why could I be having only NAs for p_val and p_val_adj in Seurat DGE analysis?
RNA-Seq R rna-seq next-gen gene
5 weeks ago by charlesgwellem • 0
5,977 results • Page 1 of 120
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Answer: What Tools/Libraries Do You Use To Visualize Genomic Feature Data?
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Recent Replies
Comment: Trimmomatic-0.36 not finding adapter directory by GenoMax 99k
Order of `fastq` file names is important for `trimmomatic`. Make sure that is correct.<br> Does `ls -lh /usr/local/bin/Trimmomatic-0.36/` …
Answer: What Tools/Libraries Do You Use To Visualize Genomic Feature Data? by cicindel ▴ 70
No love for [Tablet][1]? I'm quite surprised to not see it mentioned here. Of course, IGV is the classic, and Tablet is a bit simpler than …
Comment: How to download raw sequence data from GEO/SRA by cicindel ▴ 70
I tried to use the SRA toolkit a few months ago, I succesfully installed it and used `prefetch` to get the data, as per their tutorial, but…
Comment: Concatenating fasta files based on prefix ? by cpad0112 15k
If each group has `._1_1.txt.fa` and the pattern is exactly same as in OP, try this: ls *1_1.txt.fa | while read line; do echo ${line%…
Comment: Bioinformatics startup market analysis by grant.hovhannisyan ★ 2.1k
good luck!
Comment: Bioinformatics startup market analysis by gtechbio ▴ 30
Dear @juanjo75es, thank you for your input. We do agree that NGS data/metadata should be more accessible to public, in part also due to ini…
Comment: Bioinformatics startup market analysis by gtechbio ▴ 30
Dear @grant.hovhannisyan, thank you for the advice. In fact we are already in touch with two local genomics facilities, though as you have …
Answer: No annotation peaks when running homer by geneticatt ▴ 120
Try raising your p-value to make sure that they aren't all just being filtered out by that threshold (which seems pretty low). Edit: I may…
Comment: How to perform multiple alignment using MAFFT? by anikcropscience ▴ 40
It looks like the following: system(paste0("mafft --anysymbol --maxiterate 1000 Alignment_output/",GENE,".fa > ",GENE,".mafft.fa")) GE…
Comment: How to perform multiple alignment using MAFFT? by anikcropscience ▴ 40
Yes, I am using the following loop first in R to process all the files. This is the code that I am running first: blastn.filelist <- s…
Comment: Bioinformatics startup market analysis by grant.hovhannisyan ★ 2.1k
agreed, especially if no private information (names, clinical status, etc) is needed, this information should be freely accessible.
Comment: question when using topgo by Kevin Blighe 72k
^^ this
Answer: question when using topgo by seidel 7.6k
The GenTable() function has a parameter called *numChar* that controls this: "the GO term definition will be truncated such that only the f…
Comment: why my volcano plot looks strange? by cpad0112 15k
is it `log10p` or `-log10p` on y-axis?
Answer: How to get GO terms to specific to perticular biological process by geneticatt ▴ 120
See the 'is_a' field in the go.obo file. If you're looking for all subcategories of GO:0004553 ! hydrolase activity, hydrolyzing O-glycosyl…
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