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Hi Magdoll
I was running reconstruct_contig.py for each family and have obtained four fasta files as listed for each family.
in.trimmed.fa
cogent.fa
cogent2.renamed.fasta
cogent2.fa
I che…
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Nearly every analysis script has the same boilerplate code for direct execution via a terminal:
https://github.com/CovertLab/wcEcoli/blob/17048cb215c53d8489a4539a1722f31416925017/models/ecoli/analysi…
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i use trinity(v2.5.1) to assembly transctipts, but assemble too many unigenes, and alignment ratio is so low.
my command as below:
`Trinity --seqType fq --max_memory 10G --CPU 5 --min_contig_length …
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Hi, @Magdoll ,
I am running the `process_kmer_to_graph.py` for 'running Family Finding for a small dataset', but it reported such error like the below picture and stopped.
![image](https://user…
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The dystrophin like protein (dlp) is being employed as a hard test case while building transcriptomes for several different sea urchin species. The full length dlp mRNA is more than 13kbp and the pr…
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Hi,
I assembled a plant transcriptome from ~350M 50x50 PE reads using Trinity 2.6.6 with the following (relevant) parameters:
````
--no_normalize_reads --no_path_merging --min_kmer_cov 5
````
…
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Hi Brian,
As I mentioned during our meeting ~2 weeks ago, we have an issue that Trinity does not assemble full-length genes that should be present in the transcriptome, because we already cloned th…
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Hi,
I am working on the single cell RNA seq data from the 10x genomics pipeline. The fastq file generate by this pipeline put all the cells from one sample together. Is there any way I can demultiple…
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hi ,
I am delighted to use minimap for preprocessing when using large data. However, the number of transcripts in the different partition is unbalanced, with one of them reaching tens of thousand…
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hi, Dear
when I test reconstruct_contig.py,there is a problem as follows:
reconstruct_contig.py -h
Traceback (most recent call last):
File "/home/software/Cogent/software/Anaconda2/en…