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Recent Replies
Comment: SCTransform + Harmony in Seurat for batch correction
by
shuaizh117
▴
10
Have you tried merge the objects first and then perform SCTransform?
Comment: MAF in R
by
Ram
36k
Please accept my answer to mark the post as solved:
<img src="https://i.ibb.co/M8TCL9c/Upvote-Bookmark-Accept.png" alt="upvote_bookmark_ac…
Comment: Making a pheatmap legend with superscripts
by
swbarnes2
12k
Yeah, that works, even without grid.text,
col_ha <- HeatmapAnnotation(df = annotation, col=ann_colors, annotation_legend_param = list(…
Comment: Can I compare different RNAseq experiment DEG lists to see which experiments are
by
rachel.walters.18
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Hi and thanks for the reply!
Would you recommend performing the PCA on normalised counts?
thanks!
Comment: Can I compare different RNAseq experiment DEG lists to see which experiments are
by
rpolicastro
8.2k
Before looking at the DEGs, I would suggest starting with a PCA plot and/or the euclidean distance between the samples. This will give you …
Answer: How to search and identify the function of DEGs
by
rachel.walters.18
•
0
For GO/pathway analysis and GSEA (as mentioned in a previous reply) I've always found [webgestalt][1] really easy to use.
[1]: http…
Comment: Tool to summarise stats on supplementary reads in bam
by
rob234king
▴
610
thanks, how easy is it using the same tool to count how many alignments a read has, so from 1-10 alignments and how many alignments reads h…
Comment: Method to fill N gaps with de novo assembly
by
samuel.a.odonnell
▴
330
Agreed. Unless they are the same strain, this should probably be avoided.
Can you just use your new denovo assembly for downstream analysis?
Comment: How can I convert this format of S. tuberosum gene sequence ID - Soltu.DM.10G013
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Pierre Lindenbaum
145k
where did you get this id ? `Soltu.DM.10G013850.1`
Comment: Method to fill N gaps with de novo assembly
by
pablo
▴
210
I didn't know this tool, I will try. I also used https://github.com/malonge/RagTag
Comment: Method to fill N gaps with de novo assembly
by
Juke34
★
6.9k
maybe by cheating around with cobbler (https://github.com/bcgsc/RAILS)?
Comment: Running synteny of 2 strain.
by
dthorbur
▴
220
To my knowledge there are two types of synteny tools: anchored and alignment based (not official names, just my naming convention).
**Anc…
Comment: Method to fill N gaps with de novo assembly
by
Joe
20k
Is the reference exactly the same species/strain? If they aren't basically identical this is probably not a very good idea if you plan to d…
Comment: How to find unique and common genus by comparing 4 different files containing ge
by
Joe
20k
You have already identified in the post that you can solve this with a loop and some `grep` usage.
Spend time thinking about how you break…
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