User: new_user

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new_user0
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Posts by new_user

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Comment: C: RNAseq from circular plasmids
... Thanks for the detailed reply. My situation is a) and I think because alternative transcripts are formed outside of the annotated gene boundaries this maybe causing the problem. Also the annotation itself is poor (I could work on the .gtf file but it would all have to be done manually). Looking at ...
written 2.6 years ago by new_user0
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Comment: C: RNAseq from circular plasmids
... Sorry I'm really new to RNAseq so not entirely sure what you mean. The annotation for the circular reference plasmid sequences are provided in gtf file format. I will probably try to rotate the linear sequence so the 'genome' sits more centrally and worry about the plasmid backbone which contains th ...
written 2.6 years ago by new_user0
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Comment: C: RNAseq from circular plasmids
... Thanks for the response. This is what I meant about stitching extra sequence on the ends. I can try that but am pretty sure because reads will then multimap this will mess up the transcript assembly which uses coverage over splice junctions as input. What I really need is a split read mapper and tra ...
written 2.6 years ago by new_user0
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RNAseq from circular plasmids
... Does anyone have any suggestions for split read mapping to circular reference genomes, or whether there is a way to modify the Hisat2-Stringtie-Ballgown pipeline so it work a little better in this scenario? I’ve been analysing some RNA-seq data in which circular plasmids were transfected into human ...
assembly alignment rna-seq written 2.6 years ago by new_user0
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Pipeline transcript-level DE and isoform discovery
... I wonder if anyone can give me some advice on a potential pipeline for analysis of differential transcript-level expression and novel isoform discovery. The pilot project I am working on involves analysis of mRNA-seq data derived from a human cell line which has been transfected with various plasmid ...
rna-seq written 2.7 years ago by new_user0

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