User: John
John • 210
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Posts by John
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... I can't see anything!
thanks ...
written 10 weeks ago by
John • 210
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5 follow
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... Hi, what is the parameters I should put to download the same format GTF file like the first line of GTF file below, for mm10 ?
chr1 unknown exon 3214482 3216968 . - . gene_id "Xkr4"; gene_name "Xkr4"; p_id "P14345"; transcript_id "NM_001011874"; tss_id "TSS25485";
I can download this format us ...
written 10 weeks ago by
John • 210
• updated
10 weeks ago by
Luis Nassar • 360
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... I used featurecounts to count only exons, still the same genes are showing up as DE genes.
Do you think the problem is only in library prep (fragmentation)? or The low number of reads (due to rRNA contamination?
My question is Will I get good coverage If I do deep sequencing with the same library ...
written 11 weeks ago by
John • 210
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... Here is the screen shot! first three samples are Condition A, Second three samples are condition B. Kat6a is upregulated in Condition B (with log2FC=0.83, padj<0.01 shown by DESEQ2). I don't know why it is aligned to intronic regions. Because the sample is ribosome bound RNA. Thanks
![5'][1]
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written 11 weeks ago by
John • 210
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... Thanks, I looked at them in IGV.
> if the transcripts are fragmented incorrectly you may end up with coverage from one end (5' or 3' only).
This is not a problem. ...
written 11 weeks ago by
John • 210
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... Hi
Is this formula right to calculate actual alignment percentage of my RNA seq data? I want to find out the reads mapped only to annotated genes, my sample is from Ribosome bound RNA, so I would not have introns, I want to exclude rRNA alignments from the percentage alignment.
Alignment % ...
0
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... Yes it works! Thanks ...
written 11 weeks ago by
John • 210
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... Got it thanks. Then I should call it pairwise comparison between two condition with three replicates each. ...
written 11 weeks ago by
John • 210
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... I have control and treatment, 3 samples each. They are not paired!
P.s they’re not passive aggressive dots. Biostar didn’t allow me to comment without certain number of characters. I really appreciate everyone in the forum for helping each others! Thank you for trying to help me! ...
written 11 weeks ago by
John • 210
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... Three replicates....................... ...
written 12 weeks ago by
John • 210
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