Tweet
Does anyone know how to do use MIRA with a barcoding check prior to assembly???
-
-
The easiest way is to use the (Linux only) Roche 454 off instrument applications to divide the SFF file by MID, then follow the normal MIRA approach. -
It asks for the trace files?
Hello,
It asks for the trace files (flowgrams), which you can omit with the command
mira --project=... --job=... --notraceinfo ...other parameters... according to Bastien Chevreux
but are the flowgrams useful? Because I want to directly compare MIRA to Newbler...Or are the qual files enough?Comment
-
Are you talking about the XML clipping file from sff_extract? You can get that by running sff_extract on the MID filtered SFF file (i.e. follow the normal MIRA approach).Comment
-
'traceinfo' is just some clipping information provided as XML to MIRA.Originally posted by raw937 View Post
See http://mira-assembler.sourceforge.ne..._xml_traceinfo
As maubp has already mentioned, you need to split your SFF files according to the MIDs used before you can use MIRA (.e.g. using Roche's sfftools).
Then you can either use Roche's sfftools or sff_extract to generate MIRA compliant FASTA input files.
hth, SvenComment
-
The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist on Modified Bases...Yesterday, 07:01 AM -
Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...04-04-2024, 04:25 PM
Comment