User: grant.hovhannisyan

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Posts by grant.hovhannisyan

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Comment: C: Cufflinks analysis for transcriptome assembly
... Overexpressed genes are not necessarily pseudogenes. I my case out of 100mln reads 30mln reads were mapped to mitochondrial gene and cufflinks was getting stuck on that one. But after masking it the problem was solved. ...
written 1 day ago by grant.hovhannisyan260
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Answer: A: Cufflinks analysis for transcriptome assembly
... This is most probably because of highly expressed transcripts (like rRNA or those coming from mtDNA). To quickly check it you can summarize reads by featurecounts and see which genes have very abnormally high depth. Then you can mask that genes using `–mask-file` option in cufflinks http://cole-trap ...
written 1 day ago by grant.hovhannisyan260
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Comment: C: Dealing with multimapping reads in featureCounts
... you might try to tune parameters of aligner (like maximum number of mismatches) to reduce the multimapping rate. ...
written 1 day ago by grant.hovhannisyan260
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Comment: C: Technical replicates in RNAseq
... In your example, gene counts and totals are exactly proportional to each other twice. In real experiment, it's not always the case - imagine you did DE analysis with 10 mln reads and got 100 DE genes. If the proportionality always is the same in theory if you do the same analysis with 20 million rea ...
written 2 days ago by grant.hovhannisyan260
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Comment: C: Technical replicates in RNAseq
... I think the problem is underlying in the NGS technology itself. Imagine I sequence 10 mln reads and for a given gene I get 1 read of depth. Now if you sequence 5 mln reads, will you get 0 reads for that gene, and If you sequence 20 mln, will you get 2 reads? ...
written 2 days ago by grant.hovhannisyan260
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Comment: C: Technical replicates in RNAseq
... This is exactly what I told to my boss:) ...
written 2 days ago by grant.hovhannisyan260
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Comment: C: Technical replicates in RNAseq
... Agree and I think what important is not the seq. depth itself and the numbers we get, but rather the proportionality between them, since in the end what we compare are the relative expression values, which are basically proportions. I think it would not be wrong if you sum up read counts that come f ...
written 2 days ago by grant.hovhannisyan260
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Comment: C: Technical replicates in RNAseq
... Technical replicates in my case will be the same library sequenced on the same machine but on the different days. For our experiment we need to reach 20mln reads depth for a given sample (biological replicate). For one of the samples we reached only 10 mln. And now need to decide ether to make a new ...
written 2 days ago by grant.hovhannisyan260
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Comment: C: Technical replicates in RNAseq
... Glad to see a constructive scientific discussion here :) ...
written 2 days ago by grant.hovhannisyan260
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Comment: C: Technical replicates in RNAseq
... So who is closer to the truth?:) ...
written 2 days ago by grant.hovhannisyan260

Latest awards to grant.hovhannisyan

Supporter 2 days ago, voted at least 25 times.
Scholar 28 days ago, created an answer that has been accepted. For A: Change sequence in SEQIO
Teacher 28 days ago, created an answer with at least 3 up-votes. For C: weird STAR output, bash scripting problem
Commentator 8 weeks ago, created a comment with at least 3 up-votes. For C: gatk tool installation problem
Scholar 9 weeks ago, created an answer that has been accepted. For A: Change sequence in SEQIO

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