All Questions
13
questions
1
vote
1
answer
24
views
Why is RNASpades giving three FASTA output files instead of only one?
I'm running RNASpades for de-novo transcriptome assembly in the Galaxy workflow manager
. Instead of giving only one output of ...
- 69
1
vote
0
answers
28
views
Assessing the quality of an assembly
I am trying to run a script that assess the quality of a transcriptomic assembly, a de novo assembly using a tool called Transrate. To install the tool I followed the prompts in https://bioconda....
- 163
5
votes
2
answers
95
views
Multiple genome assemblies of the same bacterial species
I have some RNA-seq data where there are reads from the "host" as well as from several bacteria species. In this experimental context, I am interested in the host associated reads and the ...
- 4,192
2
votes
2
answers
69
views
Calling isoforms from long read data generated from partially degraded RNA
What will be the best tool to call isoforms from long read data generated from partially degraded RNA. By mistake we processed some samples with poor quality RNA to generate long read. Now we are ...
- 191
1
vote
1
answer
70
views
Assembling all transcripts for an individual gene? (using single sequence to seed the assembly)
Let's say I have a candidate gene and I believe that in an individual sample, the genome sequence differs from the reference which then interferes with alignment.
Is there a way for me to do a "...
- 1,603
2
votes
1
answer
148
views
PacBio long-reads impact in transcriptome de novo assembly?
We are strongly interested in assembly a good transcriptome of reference for a non-model organism and build a local database. We have sequenced the same individual with Illumina (150 millions of pair-...
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
0
votes
1
answer
93
views
mapping and de novo assembly of plant without reference genome
I'm studying on a plant that has no reference genome and only has one scaffold assembly and one gff3 annotation file. Can I create an index with the same assembly and gff3 in STAR and do the mapping? ...
- 1
0
votes
1
answer
935
views
Assembly by stringtie
I run this cmd
./stringtie G1_sorted.bam -B -o G1.gtf -G Triticum_aestivum.IWGSC.42.gtf -p 4 -C G1.refs.gtf -A G1.abund.tab
Error is:
...
- 31
3
votes
1
answer
487
views
Cufflinks Error: sort order of reads in BAMs must be the same
I am running Cufflinks for transcriptome assembly using the .bam file generated by Hisat2. I tried both bam and sorted bam files
...
- 195
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
6
votes
1
answer
388
views
PASA pipeline: compare experimental transcripts to the reference annotation
I would like to ask if anyone has experience in running a subset of the PASA pipeline, in particular for the reconciliation of some experimental 'transcripts' with the reference annotation.
In more ...
- 2,706