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Recent Replies
Answer: Is it possible to bulk download files from GEO repository?
by
atharvakarkare14
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10
Try using this library [GEOparse][1]
[1]: https://github.com/guma44/GEOparse
Answer: How many reads for WGS Sequencing?
by
Ruqaiya
•
0
OK. Problem solved. The problem was from my end.
Thank you both for helping !!
Comment: NGS forensics: how to know if data is fabricated
by
Mensur Dlakic
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Appreciate the suggestion, but that ship has sailed and reached the other shore. This happened 10+ years ago. To the best of my knowledge n…
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analyst
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Files are not opening in any of the computer (ubuntu/windows). I rereun snpEff annotation but still output html files are having missing im…
Comment: Figures are disappeared from html report of SnpEff
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analyst
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I reinstalled nodejs:
> sudo apt-get install nodejs
Its already up to date with version v10.19.0
Answer: NGS forensics: how to know if data is fabricated
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Prash
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Mensur, if I were you, I'd probably contact the CA directly and check with him whether they have reproduced the works recently. There coul…
Comment: NGS forensics: how to know if data is fabricated
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noodle
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Working on it - it's actually a bit difficult. Low coverage of ribosomal proteins. Low coverage of housekeeping genes ...I'm trying to find…
Comment: NGS forensics: how to know if data is fabricated
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I'm a bit against pubpeer - have you ever posted there?
My gripe with them is that the posts are heavily moderated and EDITED to the point…
Comment: NGS forensics: how to know if data is fabricated
by
Philipp Bayer
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Thanks Mensur! I'd add that in 9 out of 10 cases, you won't receive a reply to a request for raw data. That's just how scientists are, does…
Comment: How many reads for WGS Sequencing?
by
Ruqaiya
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I had downloaded the two files in a similar manner actually.
Comment: How many reads for WGS Sequencing?
by
Ruqaiya
•
0
ok, i'll try to use fastp. I have only used trimmomatic and cutadapt till now and they dont identify on its own. Except the graph in fastqc…
Comment: How many reads for WGS Sequencing?
by
Ruqaiya
•
0
got it! even if i'm doing the assembly for paired end with both the files do i have set the threshold to 1000bp ?
Comment: NGS forensics: how to know if data is fabricated
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i've been in our org trying to push such a detector, our use-case is much more limited: I want to make simulated eDNA libraries as real as …
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> What is the best method to test for differential abundance at the isoform level? Salmon returns TPM values instead of the counts which Li…
Comment: NGS forensics: how to know if data is fabricated
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benformatics
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Can you post an IGV screenshot of what this looks like?
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