User: popescuiofelia

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London, UK
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Posts by popescuiofelia

<prev • 14 results • page 1 of 2 • next >
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Dendrogram on SNPs from VCF file?
... Hi! I have tried making a dendrogram from a VCF file that contains SNP data for 20 samples. First, I tried the SNP relate software, but it was excluding all the SNPs SNP pruning based on LD: Excluding 0 SNP on non-autosomes Excluding 78,187 SNPs (monomorphic: TRUE, MAF: 0.1, missin ...
snphylo fasttree snprelate written 13 months ago by popescuiofelia10 • updated 10 months ago by sankar200410
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Comment: C: Extract read with high GC content from a bam file
... Thank you very much! I will give it a try and let you know if it worked. ...
written 13 months ago by popescuiofelia10
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Comment: C: Extract read with high GC content from a bam file
... Thank you very much! I have tried that but I am still trying to make it work. It outputs an error which looks like this: Traceback (most recent call last): File "pysam.py", line 1, in import pysam File "/home/ofelia/Documents/Sequences hard drive/Seqeuences/pysam.py", ...
written 13 months ago by popescuiofelia10
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Comment: C: Extract read with high GC content from a bam file
... Thank you very much. I first extracted mapped reads from the sorted bam file (that came from bowtie) and I added the mapped reads to the FASTQC and I still have a peak of around 55%GC content. I am working on Dictyostelium discoideum which is very AT rich (27% GC content) and the sequencing was done ...
written 13 months ago by popescuiofelia10
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All SNPs excluded with LD pruning
... Hi! I am trying to do SNP calling and clustering on 20 strains of amoeba and I am following the methods described in this paper: [paper][1] > SAMfiles of all samples were further processed using picard tools version 1.106 (http://picard.sourceforge.net). SAMfiles were sorted (SortSam.jar), duplic ...
snp analysis ld pruning written 13 months ago by popescuiofelia10 • updated 12 months ago by Biostar ♦♦ 20
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Extract read with high GC content from a bam file
... Hi! I was wondering how I can extract reads from a bam file (the paired end reads were mapped to the reference genome and then the sam file was converted to bam and sorted) that have a high GC% content. I loaded my bam file into FASTQC are I have 2 distinct peaks when analysing GC content. I would l ...
reads gc content written 13 months ago by popescuiofelia10 • updated 13 months ago by Pierre Lindenbaum127k
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Comment: C: DESeq dataset split into 2 subsets?
... Thank you for your replies! I managed to run it when I deleted the sorted.bam and merged.bam endings from the strain names. ...
written 14 months ago by popescuiofelia10
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Comment: C: DESeq dataset split into 2 subsets?
... I agree. But even with "" the command works fine when the sample is lower than 171. I still have the same problem with these changes: > colData<-data.frame(strain=c("10NC87.1","11NC96.1","12NC99.1","13NC34.2","14NC39.1","15NC52.3","16NC54.2","17NC58.1","18NC60.1","19NC60.2","1NC105.1","20 ...
written 14 months ago by popescuiofelia10
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DESeq dataset split into 2 subsets?
... I have 210 genomic DNA sequences of different strains of amoeba and I am trying to do DESeq analysis on them (I am looking for lowest logfold changes). I have mapped them, counted the number of reads per gene and loaded the dataset into R. Unfortunately, I can't make the data frame that encompasses ...
software error R written 14 months ago by popescuiofelia10 • updated 14 months ago by h.mon29k
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Comment: C: Problem with extracting read counts from RNA seq file
... Hi! I have managed to find the problem, it was actually the chromosome names. However,now I face another problem as I am trying to map the sequence to the open reading frame reference file which looks like this: >DDB0216524|DDB_G0267364 |DNA coding sequence|gene: DDB_G0267364_RTE on chromos ...
written 17 months ago by popescuiofelia10 • updated 17 months ago by h.mon29k

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