User: v27
v27 • 10
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Posts by v27
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... thank you for the code :)
...
written 8 weeks ago by
v27 • 10
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... just running on a deadline right now... ...
written 8 weeks ago by
v27 • 10
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... could you please give me the code .. i have to repeat this for 2500 files. code would make it a lot easier for me ...
written 8 weeks ago by
v27 • 10
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... i can do this in excel ..... but i have 2500 files for which i need to repeat the procedure . ...
written 8 weeks ago by
v27 • 10
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5 follow
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... I have 3 files :
File1
WP_082277722.10 gi|37527581|ref|NP_930925.1| 59.420 138 46 3 141 275 2895 3025 1.34e-41 157 49
WP_082277722.10 gi|91779924|ref|YP_555132.1| 49.254 134 56 3 151 276 2074 2203 6.02e-27 115 46
WP_082277722.10 gi|212640077|ref|YP_002316597.1| 33.981 103 57 5 180 275 ...
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... i have written a program to detect the bidirectional hit. which is as follows
query = open("abc.txt","r").readlines()
database = open("cba","r").readlines()
Q2Ddict = {}
for line in query:
Q2Ddict[line.rsplit()[0]] = line.rsplit()[1]
D2Qdict = {}
for line in d ...
written 12 weeks ago by
v27 • 10
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... I want to detect copy number variation in fungi data (paired-end, Illumina data). The data is as following:`2 sensitive
2 resistant strains
1 reference`
Could someone suggest me a tool for detecting CNV.
...
written 3 months ago by
v27 • 10
• updated
6 weeks ago by
doctor.dee005 • 130
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Comment:
C: Copy number variation detection
... thank you.
I am not working on tumor data. I have a reference fungi sequence. and four other fungi samples. I have 2 objectives:
to find the SNPs and second to find the copy number variation among genes.
I have successfully detected the SNPs using samtools and vcf tools.
I am stuck with detectio ...
written 4 months ago by
v27 • 10
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Comment:
C: Copy number variation detection
... thank you. I appreciate it. I will keep it in mind for the future. ...
written 4 months ago by
v27 • 10
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... `Hi
I trying to detect copy number variation using varscan:
the command that i used is
samtools mpileup -q 1 -f Reference.fa k_output_bowtie2.bam | java -jar VarScan.v2.3.9.jar copynumber varscan_S14 --mpileup 1
i get the following error:
[mpileup] 1 samples in 1 input files
Set ...
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