User: newbie
newbie • 70
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I have mutational data and created an oncoplot that shows the number of mutations and the type of mutation of genes in each sample.
Showing here an example plot:
![enter image description here][1]
How can I look whether DNMT3A gene mutation activating or inactivating other genes?
[1]: https: ...
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... okay. you mean in the above bam it is seen that `XS:A` is given `-` so this tells the data is strand specific? Am I right? and how based on genes we can say that? ...
written 2 days ago by
newbie • 70
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... This is PairEnd Data
Fraction of reads failed to determine: 0.0000
Fraction of reads explained by "1++,1--,2+-,2-+": 0.0047
Fraction of reads explained by "1+-,1-+,2++,2--": 0.9953
As "1+-,1-+,2++,2--" gets more signal which means fr-firststrand. So, in HISAT2 alignment step the –rna –stra ...
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... can you please help me with this...for my previous comment. ...
written 2 days ago by
newbie • 70
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... My bam file looks like this:
D00535:34:CBMGRANXX:6:2205:6601:17310 355 1 15311 1 92M = 15443 230 CTGGGGTCACAGAGCAAGGCAAAAGCAGCGCTGGGTACAAGCTCAAAACCATAGTGCCCAGGGCACTGCCGCTGCAGGCGCAGGCATCGCATGGGGEGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCGGGGGGGG AS:i:0 Z ...
written 2 days ago by
newbie • 70
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... okay I found the solution. The problem is with `chr` In the bam file it is only number. So, now I removed `chr` in gtf and converted to bed and used rseqc and got the output without any error. ...
written 2 days ago by
newbie • 70
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... gencode.v27.annotation.bed looks like this:
chr1 11868 12227 ENSG00000223972.5 . + HAVANA exon . gene_id "ENSG00000223972.5"; transcript_id "ENST00000456328.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_name "DDX1 ...
written 2 days ago by
newbie • 70
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I'm using rseqc on my samples bam file to check the strand specific. For this I used gencode gtf file. Initially I converted gencode gtf to bed file like:
This is how the gtf looks:
##description: evidence-based annotation of the human genome (GRCh38), version 27 (Ensembl 90)
##provider: ...
written 2 days ago by
newbie • 70
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... @Kevin Blighe and @genomax based on coordinates of the novel lncRNA sequence, I extracted the given region from on TCGA sample bam and visualized in IGV and I see that the lncRNA sequence aligns with the exon of a coding gene TNC. How do I proceed now? ...
written 10 days ago by
newbie • 70
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... Thanks a lot will try this approach first but do you think first I should visualise in IGV to see whether there is a possibility for expression? ...
written 11 days ago by
newbie • 70
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