User: lakshmi9c

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lakshmi9c10
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Posts by lakshmi9c

<prev • 18 results • page 1 of 2 • next >
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Comment: C: Does trimming RNA-Seq reads affect the differentially expressed genes?
... Thanks! I will try that. ...
written 10 days ago by lakshmi9c10
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Comment: C: Does trimming RNA-Seq reads affect the differentially expressed genes?
... Okay that makes sense. Could you also tell me what trimming options would be the best? Like, I chose Q score threshold as 20, but even Q=30 or Q=15 gives the same result. So how do I know which option to stick with? ...
written 11 days ago by lakshmi9c10
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Comment: C: Does trimming RNA-Seq reads affect the differentially expressed genes?
... Hi genomax, Sorry for the delayed response, I decided on Q score (Phred score) threshold as Q= 20. So any of the reads having quality below 20 will be trimmed. I chose this based the average Phred score of my reads for all my samples, which is about 30. Also, I think my data is of good quality, i. ...
written 11 days ago by lakshmi9c10
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Comment: C: Does trimming RNA-Seq reads affect the differentially expressed genes?
... Yes, the number of alignments of newly trimmed reads to the transcripts is the same. It gives the same number of alignments even after read trimming. The total number of genes, however, is the same, which you say is not unusual. Trimmomatic hasn't produced a log file, so I cannot say how many numb ...
written 27 days ago by lakshmi9c10
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Comment: C: Does trimming RNA-Seq reads affect the differentially expressed genes?
... Would that be the case even if I use different trimming options- Sliding window, MINLEN? I am trimming in the first place because I have some low quality reads in my library. That would mean trimmomatic removes those reads, and I interpreted that with FASTQC report post-trimming. Shouldn't it be ref ...
written 4 weeks ago by lakshmi9c10
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Comment: C: Does trimming RNA-Seq reads affect the differentially expressed genes?
... @ATpoint Thanks for clarifying that! However, I have another question. I have performed Trimmomatic on my paired-end reads (SLIDING WINDOW 4:20) and I am confused with the output I have got. The number of transcripts/ transcripts IDs post-trimming are exactly the same as the number of transcripts ...
written 4 weeks ago by lakshmi9c10
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Comment: C: ballgown has "." as Gene Names
... Hi, I'm facing the same issues. I'm getting the gene names for my ballgown object as "." when I run the code `geneNames(bgControl)` and texpr(bgControl, 'all')$gene_name. Can you please elaborate how fixed this issue? Did you add the gene names column in the annotation file? ...
written 4 weeks ago by lakshmi9c10
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Comment: C: How many mitochondrial genes are present in humans?
... Yes, I was made aware of [https://biology.stackexchange.com][1] [1]: https://biology.stackexchange.com forum for questions more related to biology. Thanks for your time! ...
written 6 weeks ago by lakshmi9c10
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Comment: C: How many mitochondrial genes are present in humans?
... First of all, sorry that my question isn't related to bioinformatics. Thanks for your quick response! However, I only posted this question after in-depth search and realized the list of genes I have is not elaborate. According to [wiki][1], human mitochondria has 37 genes, but there are many more ...
written 6 weeks ago by lakshmi9c10
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How many mitochondrial genes are present in humans?
... Hi, I know this might come as a silly question, but is there a definite number of mitochondrial genes in human beings? I have a list of about 68 genes, but I'm sure there are more. Can someone please help me with it? How many genes in human are involved in mitochondrial functions or are related to ...
genome gene written 6 weeks ago by lakshmi9c10

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