User: always_learning
always_learning • 790
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Posts by always_learning
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... rna_vm <- vm(rna)
Show Traceback
Rerun with Debug
Error in voom(x, d, plot = F) :
Need at least two genes to fit a mean-variance trend
I am getting above error while running vm function. Can some one help me on this ?
...
written 4 weeks ago by
always_learning • 790
0
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0
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160
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0
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Comment:
C: Extract KEGG Enzyme data
... import sys
f=open(sys.argv[1])
arr=[]
for i in f:
j = i.strip("\n").split('\t')[1]
arr.append(j)
print [arr[i:i + 3] for i in xrange(0, len(arr), 3)]
This should work for you, assuming that you files is tab seperated file. ...
written 3 months ago by
always_learning • 790
0
votes
1
answer
214
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1
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Comment:
C: Error in DADA2
... Can you try this please ?
out <- filterAndTrim(fnFs, filtFs, fnRs, filtRs, truncLen=c(240,160),
maxN=0, maxEE=c(2,2), truncQ=2, rm.phix=TRUE,
compress=TRUE, multithread=FALSE)" ...
written 3 months ago by
always_learning • 790
0
votes
1
answer
214
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1
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Answer:
A: Error in DADA2
... mc.cores > 1 is not available for windows. You may try as mc.cores = 1
something like below may work.
mcmapply(fastqPairedFilter, mapply(c, fwd, rev, SIMPLIFY = FALSE), mc.cores = 1 )
Can you please try above and let us know. ...
written 3 months ago by
always_learning • 790
• updated
3 months ago by
genomax ♦ 33k
0
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2
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294
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2
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... Hi I know about all these tools. I am moreover asking about how you will interpret results from these tools ? Is their any tutorials somewhere which can help me to understanding this ?
Thanks ...
written 3 months ago by
always_learning • 790
1
vote
2
answers
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2
answers
... Dear All,
I want to know about ROH analysis ? How to perform it ? How to interpret out put ROH resut data from tools like plink and bcftols roh etc etc. Is their any tutorial or papers available to learn understand and learn these concepts ?
Thanks
Najeeb ...
written 4 months ago by
always_learning • 790
3
votes
3
answers
348
views
3
answers
... You should use bed flle from SureSelect kit.
java -jar GenomeAnalysisTK.jar -T HaplotypeCaller \
-R '/home/dee/bioinformatics/_reffiles/hg19/ucsc.hg19.fasta' \
-I '/1234/1234_remdup_recal.bam' \
-o '/1234/1234_remdup_recal.g.vcf' \
--emitRefConfidence GVCF \
--variant_index_ ...
written 4 months ago by
always_learning • 790
0
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5
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3.5k
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5
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... As far as I know GATK doesn't do Genome Assembly.
...
written 4 months ago by
always_learning • 790
0
votes
1
answer
173
views
1
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... Thanks, Every one. I got the answer for this one actually my transcript was like
values<- c("NM_000350.2","NM_000016.5","NM_004924.4","NM_001106.3","NM_000022.2") and
it was not maching with any of records so i just converted this into
values = c("NM_000350","NM_000016","NM_004924","NM_00110 ...
written 4 months ago by
always_learning • 790
0
votes
1
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173
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1
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... library("biomaRt")
ensembl<- useMart("ensembl", dataset="hsapiens_gene_ensembl")
value =read.csv("Refseq.txt", strip.white=TRUE)
colnames(value) = c("name")
values <- as.vector(value$name)
getBM(attributes=c("refseq ...
written 4 months ago by
always_learning • 790
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