User: Annie

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Annie0
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Posts by Annie

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Comment: C: clustering sequence FASTA GSS, EST, Transcripts
... Thanks for your answer genomax, but I have found uclust to be better than CD-HIT ...
written 7 weeks ago by Annie0
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clustering sequence FASTA GSS, EST, Transcripts
... I want to do clustering (k-means) and redundancy removal of my FASTA sequences which are mainly GSS, EST and assembled transcripts, to create a reference set for my short query sequences. My short query sequences can target either DNA or RNA. So I need some expert guidance. Also should I convert low ...
genome assembly next-gen sequence alignment written 7 weeks ago by Annie0 • updated 4 weeks ago by Biostar ♦♦ 20
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Bacterial transcriptome with Rockhopper
... Hello there, I am facing problem in interpreting Rockhopper output. I have bacterial RNAseq data which is single end and 50 bp read length. Reference database is available. There are duplicates for both the samples. I ran Rockhopper using following parameters checked "Reverse complement reads" and " ...
rockhopper rna-seq q-value fold-change written 14 months ago by Annie0 • updated 14 months ago by WouterDeCoster40k
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Comment: A: resequencing RNAseq single end reads (Source: Bacteria)
... Thanks for swift reply, but my strain is H37Rv. will it be good to go with featureCounts? ...
written 14 months ago by Annie0
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resequencing RNAseq single end reads (Source: Bacteria)
... Hi everyone, I am new to NGS data analysis. I have got RNAseq data of read length 50, and single end, which I need to do resequence with the reference genome of Mycobacterium tuberculosis. first thing I did is, I ran Rockhopper, which gave me transcripts.txt and operon.txt files. Now I want to do re ...
resequencing cufflinks mtb rna-seq rpkm written 14 months ago by Annie0

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