User: Bastien Hervé

gravatar for Bastien Hervé
Bastien Hervé2.7k
Reputation:
2,700
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Location:
Limoges, CBRS, France
Last seen:
2 hours ago
Joined:
1 year, 10 months ago
Email:
b****************@orange.fr

Posts by Bastien Hervé

<prev • 552 results • page 1 of 56 • next >
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Comment: C: htseq-count SAM Processing error "can't decode byte 0xa7"
... Try this on a single sam result that failed and compare the two lines ...
written 22 hours ago by Bastien Hervé2.7k
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Comment: C: htseq-count SAM Processing error "can't decode byte 0xa7"
... 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 Hervé2.7k
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Comment: C: htseq-count SAM Processing error "can't decode byte 0xa7"
... 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 Hervé2.7k
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Comment: C: Omics Data Analysis: What keeps you up at night
... awful design experiment : no replicate or replicates on the same flowcell ...
written 1 day ago by Bastien Hervé2.7k
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Comment: C: htseq-count SAM Processing error "can't decode byte 0xa7"
... 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 Hervé2.7k
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Comment: C: STAR Splice Junctions normalization
... 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 Hervé2.7k
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Comment: C: htseq-count SAM Processing error "can't decode byte 0xa7"
... 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 Hervé2.7k
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Comment: C: htseq-count SAM Processing error "can't decode byte 0xa7"
... > 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 Hervé2.7k
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Comment: C: STAR Splice Junctions normalization
... 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 Hervé2.7k
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Comment: C: STAR Splice Junctions normalization
... 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 Hervé2.7k

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