User: Pin.Bioinf
Pin.Bioinf • 150
- Reputation:
- 150
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- Trusted
- Location:
- Malaga
- Last seen:
- 13 hours ago
- Joined:
- 1 year, 4 months ago
- Email:
- i*************@gmail.com
Im a Health Engineer with a Bioinformatics specialization doing epigenetics research.
Posts by Pin.Bioinf
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... Hello,
A few months ago I was using lncPath in order to find pathways for lncRNAs by association of these lncRNAs to protein coding genes by association in networks. This was a good package, but it has been deleted due to removal of another package 'samr' which was one of the options of significan ...
written 15 hours ago by
Pin.Bioinf • 150
• updated
14 hours ago by
zx8754 ♦ 5.0k
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... Thank you for all your help ...
written 6 days ago by
Pin.Bioinf • 150
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... It does not seem like there is a difference as good and bad samples do not appear even close to each other, so I think the reason i dont get any DE genes is because there are none that are significant enough. But as I am new to this and the biologist is saying that there is no way there are no DE ge ...
written 6 days ago by
Pin.Bioinf • 150
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... ![PCA with batch info][1] [here][2]
![PCA without batch info ][3] [here][4]
[1]: https://ibb.co/evdnUz
[2]: https://ibb.co/evdnUz
[3]: https://ibb.co/dchswe
[4]: https://ibb.co/dchswe ...
written 6 days ago by
Pin.Bioinf • 150
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... Yes, I did. By adding the batch information to the formula I only get 1 DE gene now! ...
written 6 days ago by
Pin.Bioinf • 150
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... You mean add the batch parameter to the formula? Is that enough to solve batch effect? ...
written 6 days ago by
Pin.Bioinf • 150
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... Hello,
I am doing a differential expression analysis, and first my group sequenced 8 samples of responders and non responders to a treatment, and asked that I analyze and get the DE genes (25 DE genes). After that, they sequenced 8 samples more, and now we get 4 DE genes, no gene matches the DE gen ...
written 6 days ago by
Pin.Bioinf • 150
• updated
1 day ago by
Biostar ♦♦ 20
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... This is the table of some of the samples after mapping:
Sample Name % Aligned M Aligned
I_S1 4.7% 1.0
I_S2 48.7% 3.2
I_S3 49.0% 3.0
I_S4 46.6% 7.6
I_S6 82.4% 49.3
...
written 10 days ago by
Pin.Bioinf • 150
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... Hello Corentin,
thank you for your detailed answer. Then, looking at the % of uniquely mapped reads should be enough? How can I decide if the percentage of uniquely mapped reads is good enough for analysis? ...
written 10 days ago by
Pin.Bioinf • 150
0
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... So how do i know if my fastq file is good enough for differential expression analysis? This sample mapped 4,7% of reads against reference ...
written 10 days ago by
Pin.Bioinf • 150
Latest awards to Pin.Bioinf
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14 days ago,
created an answer that has been accepted.
For A: STAR --quantMode GeneCounts function
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