no index file is generated by default only CT and GA folders are generated. what to do?
I have big wig file of RNA seq and BS seq data.I want to calculate number of overlapping reads of RNA seq that covers the methylated CG. Which function should I use to count number of overlapps
03 April 2016 9,893 2 View
I am using pandas in Python. I have a dataframe: col1 col2 col3 col4 col5 col6 col7 Variance Mean chr1 1002 NA NA 2 3 4 ...
03 April 2016 6,808 1 View
I have 100 RN A seq samples and i have mapped them using tophat. but the alignmnet is so so. like given below: Left reads: Input : 24818 Mapped : 1562 ( 6.3% of input) of these: 122 ( 7.8%) have...
02 March 2016 7,833 4 View
I am using Encode chipseq .bam file as a control and when i make tag directory of it by using homer s/w it gave me low enrichment with lots of background. Is this sample is good to use for...
02 March 2016 7,051 0 View
I am quite new in this area and I dont understand what to do exactly.I have drawn 20,000 histograms by using for loop but i m not understanding how to analyse them together for unimodality and...
02 March 2016 3,444 1 View
NM_001081462 chr5 134833230 134833830 0 - 12.5NM_001081463 chr5 134833230 134833830 0 - 12.5NM_001081464 chr5 134833230 134833830 0 - 12.5NM_001081465 chr5 134833230 134833830 0 - 12.5NM_001081466...
02 March 2016 2,214 1 View
I have RNA sequencing files and i want to check the gene expression of all genes from that file? I want to know how can i get genes from that rna sequence files? Although it is a basic question...
02 March 2016 5,809 5 View
I want to get the output of tophat in a new directory each time instead of its by default directory ./tophat_out. For this i have also added to tohat command -o directory_name but every time it...
02 March 2016 245 5 View
I want to gather methylation column from 100s of BS sequences files into a single file in a way that the first column should be the name of genes and the other 100 columns are the methylation...
02 March 2016 5,969 3 View
I have RNA seq data which I have mapped using tophat. but the alignmnet of these sequences is very poor . How many aligned reads should be there for selection of RNA sequneces.can it be more than...
02 March 2016 9,696 5 View
I have reverse sequences (AB1 format), can I base on reverse DNA sequences to perform nucleotide alignment, convert nucleotides to amino acids and deposit the sequence in GenBank database?
11 August 2024 5,138 1 View
I'm cloning a fragment of 3200 nts into plasmid. The cloning was successful, however, 02 amino acids were mutated. Now I want to fix these 02 aa by site-directed mutagenesis technique using...
08 August 2024 4,645 2 View
I aim to be as skeptical as possible regarding whether a pair of orthologous genes results in the same phenotype in their different but related bacterial organisms under similar environmental...
05 August 2024 6,787 4 View
I have been attempting to extract DNA from Bacterial, Fungal and Yeast banked samples (>1e7 cells) using Prepman Ultra reagent and I seem to be struggling to obtain a sequence. Although the...
01 August 2024 2,079 0 View
Dear all, I am working on particle deposition in human's & rat's respiratory airways using CFD and I am looking for the 3D CAD file for my simulations (STEP or IGES format). If somone has such...
29 July 2024 1,092 2 View
Hi all. As a beginner in ChIP-seq experiments, I hope you understand that the following questions might be somewhat basic. I am planning to perform ChIP-seq or MeDIP-seq analysis to investigate...
28 July 2024 6,938 1 View
Gene sequencing related trouble shooting
25 July 2024 4,149 2 View
In running two-dimensional gel electrophoresis on bacterial protein, some spots that appear to match a protein sequence have a significantly more acidic isoelectric point than the calculated pI....
24 July 2024 8,076 3 View
Dear Researchers, My question is associated with the "MDCI" method in Orca. Please let me clarify my question using a simple example: Suppose we are going to perform CBS extrapolation using "!...
21 July 2024 1,632 0 View
Hello researchers, Sorry for my stupid question. I am learning the QIIME2 workflow for analyzing some 16s amplicon NGS fastq data. I found a very nice paper with data and code public available...
20 July 2024 5,405 2 View