User: Bastien Hervé
Bastien Hervé • 2.7k
- Reputation:
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- Limoges, CBRS, France
- Last seen:
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- Joined:
- 1 year, 10 months ago
- Email:
- b****************@orange.fr
Posts by Bastien Hervé
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... Try this on a single sam result that failed and compare the two lines ...
written 22 hours ago by
Bastien Hervé • 2.7k
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... I think that with this command :
tr -cd '\1-\176' < D8_Bird8_42-3p.sam > sample.sam
You removed what is not in 1-176 ...
written 23 hours ago by
Bastien Hervé • 2.7k
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... If you can't see the non ascii characters by eye, it's propably the non-breaking line space as ascii 160. Try your `tr` command and only remove the character 160, to see if you got multiple non ascii character or just this one ...
written 1 day ago by
Bastien Hervé • 2.7k
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... awful design experiment : no replicate or replicates on the same flowcell ...
written 1 day ago by
Bastien Hervé • 2.7k
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... Did you moved these bad bam from window to linux or vice versa ?
You could try to focus on a "bad" bam.
For each error you get extract the alignment, copy it in a text file, and re-run till your bam is working or till you get enought alignment to compare them closely (5 to 10 alignments)
Look at ...
written 2 days ago by
Bastien Hervé • 2.7k
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... Nah, let's say I have 2 conditions :
- Condition 1) normal mouse
- Condition 2) modified mouse to force the splicing events between two genes -> geneA and geneB
The forcing splice event only occurs between these two genes, everywhere else in my modified mouse should have the same amount of sp ...
written 2 days ago by
Bastien Hervé • 2.7k
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... Be aware !
This is Quality :
GJGAFGDGIIJJIJHIJHICHIGCHEGGHGIIJJCHGHFHIGIIEEIIHIGDCHEGEEFGHHFFDCDFFEEE>3;
This are TAGs :
NH:i:1 HI:i:1 AS:i:143 nM:i:1 MD:Z:75
And Quality as well as TAGs can not have lower case character (except the `i` for TAGs)
This is why the :
nM: ...
written 2 days ago by
Bastien Hervé • 2.7k
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... > Especially since most of the samples work fine in htseq-count
You got htseq-count output results for some bam of your experiment ?
> It is odd that the QUAL field has a lower value character in it
What do you mean by `has a lower value character` ? Put an example please
How many bam are ...
written 2 days ago by
Bastien Hervé • 2.7k
0
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... I've got counts, but Fisher's exact test is a test to see if I need to normalize my counts. If I got p-value < 2.2e-16, how can I normalize those counts ? ...
written 2 days ago by
Bastien Hervé • 2.7k
0
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... Thanks, I used STAR first to map my reads so I was looking for something along STAR
But this do not answer the title of this thread :) What is the good method to normalize this kind of counts ? ...
written 2 days ago by
Bastien Hervé • 2.7k
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