User: tianshenbio

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tianshenbio50
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Posts by tianshenbio

<prev • 88 results • page 1 of 9 • next >
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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 5 weeks ago by tianshenbio50
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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 5 weeks ago by tianshenbio50
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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 5 weeks ago by tianshenbio50 • updated 5 weeks ago by JC11k
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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 12 weeks ago by tianshenbio50 • updated 11 weeks ago by Hugo290
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Comment: C: How to visualise KEGG pathway?
... Thank you for your reply. It does the work! ...
written 12 weeks ago by tianshenbio50
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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 12 weeks ago by tianshenbio50 • updated 5 weeks ago by bigmawen340
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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 3 months ago by tianshenbio50
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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 3 months ago by tianshenbio50 • updated 27 days ago by Biostar ♦♦ 20
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How to specify -s option in RNAhybrid to predict miRNA targets?
... I am now using command-line RNAhybrid package to predict miRNA targets using the following command: RNAhybrid -c -p 0.05 -m 10000 -s 3utr_fly -t my_utr.fa -q my_miR.fa There is a species option ‘-s’ to tell RNAhybrid to quickly estimate statistical parameters, assuming the 3UTR are from either ...
sequence rnahybrid rna-seq mirna written 3 months ago by tianshenbio50
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Comment: C: Compare expression level of isoforms among conditions - TPM or deseq2 normalised
... Hi, thank you for your reply and the links, will definitely read more about it. Do you mean the transcript counts generated by salmon are not a real representative of transcript expression? I think salmon is able to assign reads to the transcripts where they originated, so reads mapping to overlappi ...
written 3 months ago by tianshenbio50

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