User: tianshenbio

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tianshenbio70
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Posts by tianshenbio

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Comment: C: RNA-seq raw data lost
... Thank you guys for the responses. I don’t think I will resequence the missing data (also my PI won’t pay for it for sure). I did very little trimming, just removed the adaptors and trimmed a little bit towards the 3’ end. Only ~200 reads were discarded in each trimmed file...So that’s almost the sa ...
written 19 days ago by tianshenbio70
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RNA-seq raw data lost
... I sequenced 64 samples and I accidentally erased all of my raw data...The sequencing company is able to recover only 35 out of 64. But I do have all the trimmed data (after trimmomatic) Will it be a problem to publish a paper using these data? ...
next-gen sequence rna-seq sequencing written 19 days ago by tianshenbio70 • updated 19 days ago by GenoMax92k
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Comment: C: Can I directly blast mRNAs against nr database or I need to convert it to cds fi
... Hi, yes I am actually using the blastx function within diamond. ...
written 3 months ago by tianshenbio70
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Comment: C: Can I directly blast mRNAs against nr database or I need to convert it to cds fi
... Thank you for your reply. Will give it a try. ...
written 3 months ago by tianshenbio70
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Can I directly blast mRNAs against nr database or I need to convert it to cds first
... Now I have a fasta file of mRNAs (all exons with UTRs) that I hope to annotate. Is it necessary to find the start and stop codon and blast only the CDS region to the NCBI nr database using blastx command-line tool? ...
genome annotation rna-seq blast written 3 months ago by tianshenbio70 • updated 3 months ago by JC12k
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How do I remove certain sequences in fast based on header?
... I have a fasta file like this: >XM_0000001.1 actact >XR_0000001.1 atcatc How do I remove all the sequences with a XR header? I only want to keep: >XM_0000001.1 actact ...
fasta sequence rna-seq written 5 months ago by tianshenbio70 • updated 5 months ago by Hugo340
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Comment: C: How to visualise KEGG pathway?
... Thank you for your reply. It does the work! ...
written 5 months ago by tianshenbio70
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How to visualise KEGG pathway?
... I am working on a non-model organism and I have already got the enriched kegg pathway and the associated enzymes. Is there a tool I can use to generate a pathway figure highlighting the enzymes (with ko numbers) associated with the enriched pathway? I know there are tools such as pathview but all of ...
enrichment kegg rna-seq written 5 months ago by tianshenbio70 • updated 3 months ago by bigmawen350
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Blast: use best hit or top20 hits?
... This question confused me a lot. I am blasting my transcriptome against NCBI nr database, then I will use blast2go for GO annotation. Should I only use the top hit or the top20 hits for it? Someone told me I should use top20 since the top one is not necessarily the best to describe my query sequen ...
annotation blast blast2go go rna-seq written 5 months ago by tianshenbio70
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What would be the best strategy to merge the GO annotation from blast2go, InterProScan, and eggnog
... I have a newly constructed transcriptome blasted against NCBI nr database, Now I am using three tools to perform GO annotation, interproscan, blast2go, and eggnog. I wonder if there is a proper way to pool the results? I tried to merge the results in omicsbox (blast2go), I can see some terms that ar ...
interproscan go blast2go rna-seq eggnog written 5 months ago by tianshenbio70 • updated 3 months ago by Biostar ♦♦ 20

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