User: agata88

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agata88720
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Posts by agata88

<prev • 311 results • page 1 of 32 • next >
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Comment: C: Prokka bacteria genome annotation
... Yes, I used CD-HIT, it resulted in 10905 clusters from 10942 contigs. This is not a single case, most records are multiplied. ...
written 4 days ago by agata88720
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Prokka bacteria genome annotation
... Hi all! I was annotating bacteria genome with prokka. At the end It gave me a results, which are not very understood for me. Maybe somebody more familiar with this program will help? I have multiple contigs assigned to the same annotation. I run this command: ./prokka --outdir contigs_prokka ...
prokka written 4 days ago by agata88720
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Comment: C: BWA gives wrong number of input sequences
... Hey, thanks! Do you know how can I find which sequences mapped to different contigs? Best, Agata ...
written 6 days ago by agata88720
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BWA gives wrong number of input sequences
... Hi all! I was trying to map sequences to genome contigs. To do that I've performed commands: bwa index ref.fasta bwa mem ref.fasta input.fasta > aln.sam samtools view -Sb aln.sam > aln.bam samtools sort aln.bam > aln_sorted.bam samtools flagstat aln_sorted.bam > aln ...
bwa written 6 days ago by agata88720 • updated 6 days ago by swbarnes23.9k
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Comment: C: Pipeline for de novo analysis of bacteria genome
... Thank you very much. Best, Agata ...
written 8 days ago by agata88720
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Comment: C: Pipeline for de novo analysis of bacteria genome
... Thanks for suggestions. I will try that. But before, I am going to assemble reads into contigs with Abyss. A a result I will have a lot of contigs being duplicated, what tool would you recommend for contig clustering? For rnaseq de novo I found Corset (https://github.com/Oshlack/Corset/wiki). Do yo ...
written 8 days ago by agata88720
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Pipeline for de novo analysis of bacteria genome
... Hi all! What methodology do you use for de novo analysis for bacteria genome? I don't have reference sequence of bacteria genome, and would like to annotate all found proteins, RNAs, etc. in GFF or GenBank format. Thanks for any suggestions, Agata ...
genome bacteria written 9 days ago by agata88720
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Comment: C: BWA or STAR for RNAseq?
... I became confused so I asked the Author of Super Transcripts, and the answer is here: https://groups.google.com/forum/#!category-topic/oshlack-lab/supertranscript-analysis/aoSwVvo4IMQ ...
written 14 days ago by agata88720
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Comment: C: BWA or STAR for RNAseq?
... I was following this tutorial: https://github.com/Oshlack/Lace/wiki/Example%3A-Differential-Transcript-Usage-on-a-non-model-organism ...
written 14 days ago by agata88720
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Comment: C: BWA or STAR for RNAseq?
... I used it to create long genes. After Trans-Abyss I have 163684 contigs. I wanted to create some kind of scaffolds and ended up with super transcripts since there is no reference to assemble. At the end I have ~3000 super transcripts for which 70% have blastp hit. ...
written 14 days ago by agata88720

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