User: newbie
newbie • 90
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Posts by newbie
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C: Interpretation of two PCA plots
... Thanks for the answer. I understand that they are still similar, may I know why they are mirror images?
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written 5 hours ago by
newbie • 90
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Hi,
I am working with a cancer type dataset. There are in total 250 samples. All these samples are classified into 6 groups. And I plotted a PCA plot with `Gencode Protein coding genes` and it looks like below:
![enter image description here][1]
Similarly, I also plotted a PCA with only `Gencode ...
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... Thanks a lot...it looks fine now. ...
written 7 days ago by
newbie • 90
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... Can you please show me how to do that? ...
written 7 days ago by
newbie • 90
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Hi,
I have 120 `sorted.bam` files. I would like to check the strandedness of each sample. Whether unstranded or stranded. All 120 sorted.bams are in this directory `/data/bams`
For that, I kept all the sample names in the `samples.txt` file. And I started using a shell `sbatch` script like below ...
written 7 days ago by
newbie • 90
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... I have 600 fastq.gz files. Could you please show me one example how to use `SortMeRNA` on .fastq.gz file please. thanq ...
written 21 days ago by
newbie • 90
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... In my command I haven't used `-t`. So it should also count all the lncRNAs also. ...
written 21 days ago by
newbie • 90
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... I have data from 300 tumor samples. And for all I see that genomic origin of reads are higher in intronic region. ...
written 21 days ago by
newbie • 90
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... I see that higher intronic mapping rate is see with rRNA removal. Here wee used Ribo Zero tool kit. Equal distribution of reads mapping to intronic, exonic and intergenic regions suggests that there is DNA contamination. I got this information Fromm here [rna-seq QC tutorial][1] same seen here too [ ...
written 21 days ago by
newbie • 90
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... I'm using rnaseq data (paired-end and strand-specific) which is rRNA depleted with Ribo-Zero Gold rRNA Removal Kit. I observed that most number of reads are intronic (genomic origin), which is due to Ribo-Zero.
I did the alignment with `Hisat2`. Quality check of the alignment was done with `RNA-seq ...
written 21 days ago by
newbie • 90
• updated
21 days ago by
rpolicastro • 2.0k
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