All Questions
Tagged with assembly transcriptome
14
questions
1
vote
1
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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
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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
2
votes
1
answer
40
views
How to find specific types of assemblies for specific species using entrez tools?
How to find specific types of assemblies for specific species using entrez tools?
Task: Trying to specifically find transcriptomes and associated cDNA data for a list of speices.
I can use this ...
- 217
0
votes
1
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80
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Length of Contigs in Transcriptome and Whole Genome Assembly
Why are there shorter contigs from transcriptome assembly than from a whole genome assembly? I know the difference between transcriptome and genome, but don't really understand what contigs are in the ...
- 13
1
vote
1
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515
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Trinity assembly from many samples
When you combine samples for de-novo transcriptome assembly with Trinity, do you suggest limiting the number of reads for each sample? I had read one of Matthew MacManes' papers awhile back suggesting ...
- 151
2
votes
1
answer
148
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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
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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
0
votes
1
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935
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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
6
votes
1
answer
76
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What is the current state-of-the-art in assembling hybrid transcriptomes?
We are considering attempting de novo assembly of a species transcriptomes (i.e. without a reference genome) using the combined NGS outputs of Iso-seq and Illumina.
One example I saw (Li et al 2017),...
- 3,331
4
votes
2
answers
430
views
Merge / Reconciliate several de novo transcriptome assemblies with different kmers
I am building a De Novo transcriptome reference assembly for an eukaryotic organism for which I have a genome.
I've created several assemblies with rnaSpades using different kmer sizes (19 to 69 with ...
5
votes
2
answers
399
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Reduce number of transcripts in a highly variable de novo transcriptome assembly
I have a de novo assembly using both multiple SRA and locally sequenced transcriptomes. I started with 270M PE reads from 9 tissues. Here are the assembly stats generated with ...
- 309
2
votes
1
answer
132
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Correct way to assemble reference transcriptome - what's --samples_file option in Trinity?
I have 101 samples from 9 tissues of a nonmodel species, coming either from SRA or sequenced by my lab. I want to generate a reference transcriptome with Trinity for further analysis. In order to do ...
- 309
5
votes
2
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1k
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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
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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