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Giacomo Rocchetti
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ctdarwell
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Recent Replies
Comment: How to install PEERTOOLS in a cluster?
by
fernandogs97
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0
4.0.4 version but also tried with 2.5 and 3.5 version without success
Comment: Do you need to define adapter sequences for trimming and QC tools?
by
amy__
▴
20
Thank you!!
Comment: EGA (ENA) database wont accept fastq files
by
Michael Dondrup
51k
What happens if you use only one line per pair (Just a wild guess)? Like so:
GM12878_clone4 PRJEB52794 Illumina NovaSeq 6000 gm128…
Comment: Strange Trimmomatic behavior
by
ctdarwell
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0
I will try to find out - thanks for your input
Comment: EGA (ENA) database wont accept fastq files
by
lieven.sterck
13k
I usually work via the webin interface, and not with uploaded spreadsheets but ok.
Can you check/confirm a few things? :
* you are sure th…
Comment: Strange Trimmomatic behavior
by
lieven.sterck
13k
yes, because adapter trimming will (normally) not remove anything from the 5' end of a read.
Do you have any idea how the fragmentation wa…
Comment: Limma for paired and unpaired samples. Strange number of DEGs in unpaired sample
by
Gordon Smyth
★
4.4k
Cross-posted to https://support.bioconductor.org/p/9144454/
Comment: How to install PEERTOOLS in a cluster?
by
solomoncharles77
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90
What version of R are you using?
Comment: Strange Trimmomatic behavior
by
ctdarwell
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0
Hi so I calculate they're present in around 97% of reads. Yes, at 5' end, I tried with TruSeq3 and they're still there. Thanks
Answer: Limma for paired and unpaired samples. Strange number of DEGs in unpaired sample
by
Gordon Smyth
★
4.4k
You have a paired experimental design, so naturally you get more powerful results from a paired analysis. It isn't correct to treat a paire…
Comment: How can I convert this format of S. tuberosum gene sequence ID - Soltu.DM.10G013
by
Sanja
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0
http://spuddb.uga.edu/dm_v6_1_download.shtml
I used this - ''Improved genome assembly and annotation (v6.1) for the doubled monoploid pot…
Comment: Strange Trimmomatic behavior
by
ctdarwell
•
0
Hi thanks - it's paired-end, is that what you mean by protocol? I see no mention of what adapters were used but the report doc states: "*As…
Answer: Execute commands in Bash Chunk in Rmarkdown
by
ariel
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190
In case anyone else comes along here, the "proper" way is to set the engine opts either globally or in every chunk.
For example:
~~~
…
Comment: Strange Trimmomatic behavior
by
lieven.sterck
13k
you do mean 'start' as that it is present on the 5' end of the reads?
If so, it would be really strange to be adapters as they typically d…
Comment: bcl2fastq with unique dual indexing
by
ginlucks
▴
10
Hi, thanks for answering.
I did the reverse complement of I5 index (just a simple R script) because I saw that in the resulting undetermin…
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