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Forum: Metagenomics 06-27-2018, 03:15 AM
Replies: 0
Views: 1,007
Posted By MariaF
Statistical analysis of Centrifuge output

What type of statistics should I use to analyze output from metagenome classifier "Centrifuge"?
I have run Centrifuge on 24 samples from RNA-seq: 11 samples are a grade A of the disease, 11samples...
Forum: Bioinformatics 03-28-2018, 07:32 AM
Replies: 5
Views: 867
Posted By MariaF
Thanks for your attention to my problem, GenoMax....

Thanks for your attention to my problem, GenoMax.

samtools view -H temp.samheader.sam


samtools view -H test_genome.bwt.samheader.sam


samtools view -H accepted_hits.bam
Forum: Bioinformatics 03-28-2018, 01:20 AM
Replies: 5
Views: 867
Posted By MariaF
Thanks, GenoMax, you are absolutely right: my...

Thanks, GenoMax, you are absolutely right: my annotation was Ensembl and my .fa was UCSC.

I downloaded the annotation from http://genome.ucsc.edu/cgi-bin/hgTables - is it correct?

head my .gtf...
Forum: Bioinformatics 03-23-2018, 05:14 AM
Replies: 5
Views: 867
Posted By MariaF
Reads are 0 in htseq-count

Hello,

I have a trouble using htseq-count, I used TopHat to aling my data, but when I tried to count the number of reads all the genes present 0 read.

I checked the chromosome names in ./gtf...
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