All Questions
Tagged with assembly sequence-annotation
6
questions
2
votes
1
answer
78
views
Sanger sequencing annotation error
I am a student in a Cancer lab. Working with sanger is new to me. While analyzing a report we found an insertion that has not been reported in any databases so far, we were working on checking if the ...
user16732
1
vote
3
answers
98
views
How can I assemble my genome from raw files?
I've had my whole genome sequenced (at 30x average coverage) by a lab, and they have provided the raw files to me (BAM, FASTQ, and VCF).
How can I assemble it?
And does assembly provide any further ...
- 111
0
votes
2
answers
156
views
Genome annotation
I have helped a lab sequence a mitochondrial genome. I used then MITOS to annotate the genome (warning them that I did it just for curiosity as I am not experienced). They submitted the sequence and ...
- 359
1
vote
1
answer
198
views
Decontaminating RNA seqs for de novo transcriptome assembly and annotation of novel eukaryotes
I have raw paired-end RNA-seq reads for two novel eukaryotic species. Some background: the reads represent a copepod (arthropod) species each. The mRNA for each read set was obtained by extracting ...
- 111
1
vote
0
answers
159
views
Gffcompare issue: 0 reference transcripts loaded
I am trying to use gffcompare to compare my assembled transcriptome to a reference gtf that contains information about small open reading frames (sORFs). The reference gtf was obtained by processing ...
- 31
5
votes
2
answers
1k
views
Difference between de novo transcriptome assembly methods
I have been looking around (including read the original papers) to understand what is essentially the difference between StringTie in non-reference based mode (de novo) and Trinity de novo assembly. I ...
- 111