User: sumithrasank75

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Posts by sumithrasank75

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maftools - no chromosomal coordinates
... I have a file of genes and alterations but there are no chromosomal cooridinates associated with those alterations. Can I used maftools on this file. Here is the first line of the file that I have Tumor_sample_Barcode gene alteration type mut_type 200_B NF1 ...
R bioconductor snp written 7 months ago by sumithrasank75120 • updated 5 months ago by Biostar ♦♦ 20
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converting log-odds ratio to p-value in HOMER
... I used scanMotifGenomeWide.pl for a certain motif and the output is a bed file which reports the log-odds score for finding the motif at a given chromosomal location. I want to know how to convert the log-odds ratio to a p-value so that I can filter the bed file by a p-value cutoff. Thanks ...
chip-seq written 11 months ago by sumithrasank75120
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Identify TF binding sites genomewide
... What is the best tool to use to get the genomic coordinates (as a BED file) of the binding sites of a transcription factor? I would like to do this genomewide. ...
genome sequence next-gen written 12 months ago by sumithrasank75120 • updated 12 months ago by Alex Reynolds27k
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getting a list of alignment with a particular bam tag from a bam file
... I have a list of values for a bam tag called XC (say needed.txt). I would like to extract the alignments which have these values from a bam file (say bamfile.bam). I would like to use pysam to do this, but could not figure out from the documentation how to modify the samfile.fetch command for this. ...
alignment written 13 months ago by sumithrasank75120 • updated 13 months ago by Pierre Lindenbaum118k
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parsing fastq files in python
... I have multiple fastq files for different samples. Example : S_Rep1_R1.fastq S_Rep1_R2.fastq S_Rep2_R1.fastq S_Rep2_R2.fastq I want to choose all fastq files corresponding to say S_Rep1 and execute some functions. How can I write a python script which will choose all fastq files belonging to S_Rep1. ...
next-gen written 15 months ago by sumithrasank75120 • updated 15 months ago by bioExplorer3.7k
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Using monocle on dge file
... I would like to do peudo-time analysis on moncle starting with a digital expression matrix where genes are rows and cells are columns. Example E1 E2 E3 ........ F1 F2 F3..... Gene1 0 1 1 0 0 0 Gene2 1 10 1 2 3 0 ...
next-gen rna-seq written 21 months ago by sumithrasank75120
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heatmap using DESeq2
... I am trying to generate a heat map of the top differentially expressed genes between two samples. I have used DESeq2 to identify these. My code is library(DESeq2) countData = read.csv("data.txt",header = T,sep = "\t") colData = DataFrame(condition = factor(c("female","female","female","male","ma ...
rna-seq written 22 months ago by sumithrasank75120 • updated 22 months ago by cpad011211k
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Comment: C: genes close to random genomic locations
... I read through the bedtools random documentation. It uses a file hg19.genome. Is this file in bed format and how can I download it? ...
written 2.1 years ago by sumithrasank75120
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genes close to random genomic locations
... I would like to pick a 1000 random locations in the human genome (say hg19 assembly) and get a list of the genes closest to them. Can you suggest how I can go about this? ...
gene written 2.1 years ago by sumithrasank75120
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string search in fastq file
... I have a list of 20 bp sequences stored in a list called known. I have a fastq file called A.fastq, from which I cut out the relevant 20 bp region and compare against the known list. I would like to use Hamming distance as a metric for choosing the correct match i.e for every fastq read, I want to f ...
sequencing written 2.2 years ago by sumithrasank75120 • updated 2.2 years ago by Alex Reynolds27k

Latest awards to sumithrasank75

Student 6 weeks ago, asked a question with at least 3 up-votes. For searching reads with a certain sequence in fastq file
Appreciated 6 months ago, created a post with more than 5 votes. For searching reads with a certain sequence in fastq file
Popular Question 6 months ago, created a question with more than 1,000 views. For parsing a fastq file using biopython
Popular Question 6 months ago, created a question with more than 1,000 views. For greping unique reads from fastq file
Popular Question 6 months ago, created a question with more than 1,000 views. For string matching with mismatches
Popular Question 6 months ago, created a question with more than 1,000 views. For parsing a fastq file using biopython
Popular Question 6 months ago, created a question with more than 1,000 views. For greping unique reads from fastq file
Popular Question 6 months ago, created a question with more than 1,000 views. For string matching with mismatches
Popular Question 9 months ago, created a question with more than 1,000 views. For parsing a fastq file using biopython
Popular Question 11 months ago, created a question with more than 1,000 views. For parsing a fastq file using biopython
Popular Question 13 months ago, created a question with more than 1,000 views. For parsing a fastq file using biopython
Great Question 21 months ago, created a question with more than 5,000 views. For searching reads with a certain sequence in fastq file
Popular Question 21 months ago, created a question with more than 1,000 views. For greping unique reads from fastq file
Popular Question 22 months ago, created a question with more than 1,000 views. For comparing two fastq files
Popular Question 2.5 years ago, created a question with more than 1,000 views. For comparing two fastq files
Popular Question 2.5 years ago, created a question with more than 1,000 views. For searching reads with a certain sequence in fastq file
Popular Question 3.3 years ago, created a question with more than 1,000 views. For searching reads with a certain sequence in fastq file
Student 3.3 years ago, asked a question with at least 3 up-votes. For searching reads with a certain sequence in fastq file

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