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5
votes
6
replies
6.0k
views
Genome guided assembly with Trinity using STAR genome index
RNA-Seq star trinity
updated 5.8 years ago by ▴ 10 • written 8.3 years ago by ▴ 110
1
vote
2
replies
2.7k
views
Error with combining samples into matrix using abundance_estimates_to_matrix.pl
edger RNA-Seq rna-seq matrix DE
updated 7.1 years ago by 45k • written 9.7 years ago by ▴ 110
7
votes
12
replies
4.0k
views
weird STAR output, bash scripting problem
RNA-Seq STAR bash
updated 8.2 years ago by 35k • written 8.2 years ago by ▴ 110
2
votes
8
replies
6.5k
views
automated script to trim paired end RNA seq reads using Trimmomatic
RNA-Seq trimming trimmomatic loops
updated 8.2 years ago by 35k • written 8.2 years ago by ▴ 110
1
vote
2
replies
11k
views
Downloading Fastq files from ENA using FTP
fastq RNA-Seq ena
updated 2.6 years ago by 45k • written 8.3 years ago by ▴ 110
0
votes
3
replies
2.3k
views
How to see what percentage of reads remain after quality filter to a certain phred score
phred fastqc RNA-Seq quality control
8.3 years ago by nikelle.petrillo ▴ 110
1
vote
2
replies
4.8k
views
RSEM error abundance_estimates_to_matrix.pl
RNA-Seq RSEM abundance estimate
updated 8.4 years ago by ▴ 20 • written 9.6 years ago by ▴ 110
1
vote
3
replies
2.1k
views
Number of contigs does not match number in count matrix --- de novo assembly
trinity rna-seq Assembly
updated 2.2 years ago by 45k • written 9.4 years ago by ▴ 110
0
votes
1
reply
2.3k
views
Count matrix error. abundance_estimates_to_matrix.pl Error
trinity RNA-Seq count matrix DE
updated 9.3 years ago by 27k • written 9.5 years ago by ▴ 110
1
vote
1
reply
3.0k
views
trinity assembly error, run failed
trinity rna-seq
updated 2.2 years ago by 45k • written 9.5 years ago by ▴ 110
2
votes
3
replies
5.6k
views
How to determine number of contigs used in Trinity assembly?
trinity DE assembly rna-seq
updated 2.2 years ago by 45k • written 9.4 years ago by ▴ 110
0
votes
4
replies
6.9k
views
using IGV to visualize RNA seq alignment to transcriptome
rna-seq igv alignment
updated 2.2 years ago by 45k • written 9.4 years ago by ▴ 110
1
vote
5
replies
2.7k
views
differential expression analysis, trinity error
DE RNA RNA-Seq trinity
updated 9.4 years ago by 154k • written 9.4 years ago by ▴ 110
1
vote
2
replies
2.3k
views
do i need to run Trinity assembly ALL over?
trinity assembly rna-seq
updated 2.2 years ago by 45k • written 9.4 years ago by ▴ 110
0
votes
5
replies
2.1k
views
EdgeR Error, 0 gene counts for 1 sample
RNA-Seq differential expression DE edger
9.4 years ago by nikelle.petrillo ▴ 110
1
vote
1
reply
2.2k
views
Aligning Reads to Transcriptome Question
rna RNA-Seq aligning trinity
updated 9.5 years ago by 20 • written 9.5 years ago by ▴ 110
16
votes
8
replies
8.6k
views
Understanding Trimmomatic Sliding Window Approach
RNA-Seq trimmomatic quality control qc
updated 9.5 years ago by ▴ 180 • written 9.5 years ago by ▴ 110
0
votes
1
reply
2.2k
views
Trinity Assembly Timing Question
Trinity RNA-Seq assembly
9.5 years ago by nikelle.petrillo ▴ 110
7
votes
8
replies
10k
views
Determining read count
trimmomatic rna-seq trinity
updated 2.2 years ago by 45k • written 9.5 years ago by ▴ 110
3
votes
20
replies
5.1k
views
de novo RNA seq, combining left and right reads to create assembly
assembly RNA-Seq trinity transcriptome
updated 9.6 years ago by 16k • written 9.6 years ago by ▴ 110
4
votes
3
replies
7.0k
views
Using featurecounts for EdgeR input?
edger rsubread de RNA-Seq
updated 9.6 years ago by 20 • written 9.6 years ago by ▴ 110
1
vote
3
replies
2.1k
views
de novo transcriptome assembly, read length?
RNA-Seq fastqc read-length galaxy
updated 3.3 years ago by 45k • written 9.8 years ago by ▴ 110
1
vote
2
replies
2.4k
views
Tophat Parameters for RNA seq de novo
RNA-Seq tophat
9.6 years ago by nikelle.petrillo ▴ 110
4
votes
10
replies
3.5k
views
How to decipher FPKM Values?
RNA-Seq fpkm
updated 9.6 years ago by 48k • written 9.6 years ago by ▴ 110
4
votes
3
replies
8.7k
views
How to find/decipher Trimmomatic Output
trimmomatic RNA-Seq QC
updated 19 months ago by 45k • written 9.7 years ago by ▴ 110
0
votes
3
replies
4.2k
views
Question on Trimmomatic Defaults?
phred trinity rna-seq trimmomatic
updated 3.3 years ago by 45k • written 9.8 years ago by ▴ 110
5
votes
14
replies
6.3k
views
de novo transcriptome assembly work flow, paired end reads
de-novo trancscriptome rna RNA-Seq trinity
updated 3.3 years ago by 45k • written 9.8 years ago by ▴ 110
0
votes
13
replies
5.0k
views
Generating Read Length?
RNA-Seq phred-quality read-length
updated 3.3 years ago by 45k • written 9.8 years ago by ▴ 110
0
votes
5
replies
5.5k
views
align_and_estimate_abundance.pl ERROR/ QUESTION
aligning abundance RNA-Seq trinity
updated 3.5 years ago by 45k • written 9.8 years ago by ▴ 110
0
votes
1
reply
4.4k
views
rem-synthesis-reference-transcripts : No such file or directory! RSEM-EVAL QUESTION
detonate rsem RNA-Seq rsem-eval
updated 3.5 years ago by 45k • written 9.8 years ago by ▴ 110
0
votes
3
replies
3.4k
views
ERROR Running Detonate: RSEM EVAL on RNA SEQ assembly
rsem-eval rsem RNA-Seq detonate
updated 3.5 years ago by 45k • written 9.8 years ago by ▴ 110
2
votes
1
reply
6.2k
views
Installing Trinity, Error with Samtools
RNA-Seq samtools trinity
updated 3.3 years ago by 45k • written 9.9 years ago by ▴ 110
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