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4
votes
11
replies
7.7k
views
8 follow
Filtering out the spliced reads from bam file.
RNA-Seq BAM spliced-reads
updated 2.6 years ago by ★ 2.4k • written 9.1 years ago by ▴ 610
0
votes
0
replies
693
views
Genomic intervals to transcriptomic intervals
RNA-Seq bed
5.1 years ago by EVR ▴ 610
2
votes
1
reply
854
views
Statistically overrepresented gene types from Differentially expressed genes.
RNA-Seq next-gen gene-types enrichment
updated 5.3 years ago by 21k • written 5.3 years ago by ▴ 610
0
votes
2
replies
1.8k
views
LRT test in DESeq2 gives weird volcano plot
DEseq2 LRT RNA-Seq VolcanoPlot
updated 5.8 years ago by 88k • written 5.8 years ago by ▴ 610
3
votes
12
replies
5.0k
views
Counting mutated reads from RNA Seq data
Mutation Variant-analysis RNA-Seq Samtools
updated 2.8 years ago by 45k • written 9.9 years ago by ▴ 610
3
votes
3
replies
3.2k
views
Identifying miRNA, RNA-binding sites in UTRs
UTRs miNRA RNA-binding protein
updated 7.6 years ago by ▴ 520 • written 7.6 years ago by ▴ 610
0
votes
4
replies
5.8k
views
Tool for predicting RNA binding protein
RNA-Seq RNA-binding-proteins
updated 3.2 years ago by 45k • written 10.4 years ago by ▴ 610
0
votes
3
replies
2.2k
views
Merging bed intervals within a group
Bedtools bedops BED
7.9 years ago by EVR ▴ 610
5
votes
10
replies
3.5k
views
6 follow
Average intron length in Drosophila melagnoster
Drosophila Intron_length
updated 7.9 years ago by ★ 1.5k • written 7.9 years ago by ▴ 610
2
votes
5
replies
3.7k
views
IGV error: Error loading SAM header: For sequence 34711, text and binary have different lengths in file.
RNA-Seq BAM IGV
updated 8.0 years ago by ▴ 310 • written 8.0 years ago by ▴ 610
0
votes
3
replies
1.9k
views
Finding fragemented transcriptome
transcriptome denovo_assembly
updated 8.1 years ago by ★ 1.5k • written 8.1 years ago by ▴ 610
1
vote
1
reply
2.2k
views
Splitting the Spliced reads from genome Alignment
bed bedtools bedops bam Spliced_reads
8.1 years ago by EVR ▴ 610
3
votes
3
replies
3.0k
views
Indpendent Filtering in DESeq2
DESeq2 Independent filtering
updated 8.3 years ago by 105k • written 8.3 years ago by ▴ 610
5
votes
6
replies
2.5k
views
Pairwise comparision in DESeq2
RNA-Seq DESeq2
updated 8.4 years ago by 9.0k • written 8.4 years ago by ▴ 610
7
votes
8
replies
3.8k
views
Finding Batch effects in RNAseq data
RNA-Seq batch-effect
8.4 years ago by EVR ▴ 610
0
votes
2
replies
2.1k
views
Aligning reads to genome/transcriptome
RNA-Seq Tophat2 bowtie2 bowtie
8.4 years ago by EVR ▴ 610
4
votes
6
replies
5.7k
views
Extracting entries from GTF file
GTF bed
updated 8.5 years ago by 36k • written 8.5 years ago by ▴ 610
0
votes
2
replies
2.6k
views
DESeq2 Normalization of time course
DESeq2 RNA-Seq Normalization
updated 8.5 years ago by ▴ 30 • written 8.6 years ago by ▴ 610
4
votes
3
replies
10k
views
What is a "draft genome assembly"?
Genome_assembly de novo
updated 8.6 years ago by 16k • written 8.6 years ago by ▴ 610
0
votes
3
replies
1.8k
views
Computing intron length per trancript
intron_length GFF3
8.6 years ago by EVR ▴ 610
1
vote
6
replies
1.7k
views
Counting read orientation between ranges in a bed file
BED bedtools bedops
updated 8.7 years ago by 12k • written 8.7 years ago by ▴ 610
2
votes
2
replies
4.2k
views
Adding GO:IDs to the BLAST hits
Gene Ontology BLAST
updated 8.7 years ago by ▴ 20 • written 8.8 years ago by ▴ 610
0
votes
4
replies
6.0k
views
Getting BP, MF and CC from GO IDs
Gene Ontology
updated 8.8 years ago by 7.6k • written 8.8 years ago by ▴ 610
1
vote
14
replies
2.8k
views
Compairng multiple sequence and finding similarity.
DNA_Sequences Fasta Sequence_comparision
updated 8.9 years ago by 12k • written 8.9 years ago by ▴ 610
2
votes
4
replies
2.5k
views
Finding alignment score for multi-read frombam/sam file
RNA-Seq Bam Sam Tophat Multi-read
8.9 years ago by EVR ▴ 610
5
votes
3
replies
2.4k
views
Appending sequences in fasta file with identical headers
fasta
updated 8.9 years ago by 7.1k • written 8.9 years ago by ▴ 610
1
vote
7
replies
2.2k
views
Extracting reads outside the boundaries in a BED file
bed_file bedtools
updated 9.0 years ago by 36k • written 9.0 years ago by ▴ 610
0
votes
1
reply
2.5k
views
Minimum and maximum Intron length of Oryza sativa
Intron length Oryza sativa tophat2
9.0 years ago by EVR ▴ 610
0
votes
5
replies
2.4k
views
Oryza Sativa Transcriptome
Transcriptome Oryza_sativa
updated 9.0 years ago by ★ 5.2k • written 9.0 years ago by ▴ 610
2
votes
4
replies
2.7k
views
Q33 in fastx_clipper
Fastx RNA-Seq
updated 2.5 years ago by 45k • written 10.1 years ago by ▴ 610
2
votes
5
replies
2.1k
views
Evaluating the Genome aseemblies
RNA-Seq genome N50
updated 9.1 years ago by 13k • written 9.1 years ago by ▴ 610
3
votes
5
replies
9.9k
views
Finding overlapping ranges in R
RNA-Seq R Overlapping-ranges
updated 9.1 years ago by ★ 3.2k • written 9.1 years ago by ▴ 610
0
votes
0
replies
1.2k
views
Finidng the closest features near transcript boundaries in genome
RNA-Seq bedtools bedops joining-features
9.1 years ago by EVR ▴ 610
0
votes
4
replies
3.4k
views
Extracing the regions outside the target(transctip) region in genome
RNA-Seq bedtools samtools bam_file genome
updated 9.1 years ago by 20 • written 9.3 years ago by ▴ 610
2
votes
3
replies
2.5k
views
Reading bam files and extratcing transcript from abm files in R
RNA-Seq bam samtools
updated 9.2 years ago by 12k • written 9.2 years ago by ▴ 610
0
votes
4
replies
2.5k
views
Detecting the peaks from RNAseq data
RNA-Seq peak bam
updated 9.2 years ago by ★ 5.2k • written 9.2 years ago by ▴ 610
1
vote
4
replies
1.1k
views
Mappping read to its exact postion in genome
RNA-Seq TOPHAT
updated 9.2 years ago by 105k • written 9.2 years ago by ▴ 610
0
votes
1
reply
1.4k
views
Computing Genome Duplication
genome Duplication RNA-Seq
9.2 years ago by EVR ▴ 610
0
votes
5
replies
3.1k
views
Counting reads within regions of interest
bam RNA-Seq coverage
9.3 years ago by EVR ▴ 610
0
votes
4
replies
1.9k
views
Counting reads on genome
RNA-Seq genome transcriptome
updated 9.3 years ago by ★ 2.1k • written 9.3 years ago by ▴ 610
3
votes
6
replies
2.9k
views
Identifying full length transcripts in a transcriptome
de-novo-Transcriptome full-length-transcripts
updated 3.0 years ago by 45k • written 9.5 years ago by ▴ 610
1
vote
5
replies
3.5k
views
Aligning reads to genome together with transcriptome
RNA-Seq Genome Transcriptome alignment
updated 3.0 years ago by 45k • written 9.4 years ago by ▴ 610
1
vote
1
reply
4.5k
views
Generating GTF file for de novo assmebled transcriptome
GTF Transcriptome
updated 9.6 years ago by 8.4k • written 9.6 years ago by ▴ 610
0
votes
4
replies
6.9k
views
Log2 fold change heatmap
Log2foldchange heatmap Microarray
updated 2.9 years ago by 45k • written 9.6 years ago by ▴ 610
1
vote
1
reply
2.7k
views
Quality control for AB Solid fastq files
Fastqc AB-Solid RNA-Seq
updated 2.9 years ago by 45k • written 9.7 years ago by ▴ 610
13
votes
10
replies
11k
views
Finding the iIllumina index read from raw fastq file
RNA-Seq illumina index-read
updated 2.8 years ago by 45k • written 9.8 years ago by ▴ 610
0
votes
1
reply
2.6k
views
All reads deposited in Undetermined indices
RNA-Seq demultiplexing Undetermined_indices
updated 2.8 years ago by 45k • written 9.8 years ago by ▴ 610
2
votes
2
replies
3.4k
views
GO enrichment analysis on Non-model Organism
Enrichment-analysis Gene-Ontology
updated 2.8 years ago by 45k • written 9.8 years ago by ▴ 610
1
vote
1
reply
2.2k
views
calculating the coverage percentage from blast8
Coverage percentage blast8 output blat
updated 9.8 years ago by 20 • written 10.0 years ago by ▴ 610
0
votes
2
replies
2.1k
views
Extracting aligned consensus sequences for every transcript from sam file
RNA-Seq sequence bowtie-2
9.9 years ago by EVR ▴ 610
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