User: Kai_Qi
Kai_Qi • 100
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Posts by Kai_Qi
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Comment:
C: MEME cannot handle 318 sequence?
... Thanks for reply. I tried it by using maxsize 0. still get the same results， I just tried to use the first 100 line to run the code, it worked well. I guess my sequence plus the number of sequences exceed the limit of meme； then i tried too add a number of -maxsize 200000, it starts running.
...
written 20 days ago by
Kai_Qi • 100
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... Hi:
I put a fasta file for MEME like this:
meme input.fasta -mod anr -oc MEME_no_control_motif10 -rna -nmotifs 10 -minw 6 -maxw 10 > log4 2> error4
cat error4
Dataset too large (> 100000). Rerun with larger -maxsize.
The fasta contains about 318 sequences:
wc -l input ...
written 21 days ago by
Kai_Qi • 100
• updated
20 days ago by
Alex Reynolds ♦ 31k
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... Hi all:
I have an gene list after analyzing the dynamic expression. I separated them when generating clusters using arbitory numbers, say I generated 3 clusters after trying different numbers, and this cluster is so far satisfying.
I have written the files so I know which gene belongs to which cl ...
written 24 days ago by
Kai_Qi • 100
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... I have samples across 4 different developmental stages, each stage has 2 replicates. Using DEseq2, I can get the trending line of the counts of each gene, below is the code I have run:
library(DESeq2)
sampleTable <- as.data.frame(sampleTable)
countdata <- read.csv("CSHLRNASeq_coun ...
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... Here is the link for the [answer][1]:
[1]: https://www.biostars.org/p/343893/ ...
written 29 days ago by
Kai_Qi • 100
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... Sorry for posting it again:
I found the answer Kevin has shown before:
`dds <- DESeq(dds, test = 'LRT', reduced = ~ 1)` works with no error.
...
written 4 weeks ago by
Kai_Qi • 100
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... I am using DEseq2 to do differential analysis from RNA-seq data across 4 developmental stages, each stages have 2 replicates. I can following through the manual to do comparisons between each two stages. Now I want to do the comparison across 4 stages in a time series manner so that I can know the g ...
written 4 weeks ago by
Kai_Qi • 100
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... The solutions worked.
Thanks a lot. ...
written 5 weeks ago by
Kai_Qi • 100
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... I found the answer to the first part: I used `$ sed 's/>//' mycoord.csv > mycoord_1.csv` to remove ">"
$ head mycoord_1.csv
16:23107820-23108019(+)
14:54909471-54909670(-)
7:127020805-127021004(-)
X:20848619-20848818(+)
1:75547398-75547597(+)
11:102777648-102777 ...
written 5 weeks ago by
Kai_Qi • 100
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... I have a fasta file that contains the coordinates and the sequence of the coordinates:
head my.fasta
>16:23107820-23108019(+)
GTACGGCGCTCCCGGGGCGGCCGGTGGCCTGTAGTCAAGGTCACTAGGACCCGCGTTGAGGTGGGTTGCTTGGCGGCCACACTGCAGGTATGCGGGCTTTTTCTTAGGGCACACACTTCTCCTTGTGCCCTTCGAGAAGCTTCCATGATGGTAAGACT ...
written 5 weeks ago by
Kai_Qi • 100
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