I am processing some sequencing data that came from cell culture samples. There is some potential Mycoplasma contamination. If you are not familiar with working with cells, this is a very common occurrence. I think the easiest solution would be to align to Mycoplasma and see how many reads actually align. Unfortunately, there are many Mycoplasma species and genomes seem to vary widely. Is there already a pre-compiled list of reference sequences I can align to in order to check for that? Are there better solutions to check for contamination?
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
Originally posted by id0 View PostI am processing some sequencing data that came from cell culture samples. There is some potential Mycoplasma contamination. If you are not familiar with working with cells, this is a very common occurrence. I think the easiest solution would be to align to Mycoplasma and see how many reads actually align. Unfortunately, there are many Mycoplasma species and genomes seem to vary widely. Is there already a pre-compiled list of reference sequences I can align to in order to check for that? Are there better solutions to check for contamination?Last edited by winsettz; 10-24-2013, 08:26 AM.
Comment
-
Originally posted by winsettz View PostIf I remember correctly, in the lab the way to do it is by PCR. In silico, you could recapitulate that by finding the gene that is PCR'ed and screen your reads for it. Can't say what the FP/FN rate would be, but it'd be a start.
Comment
-
Originally posted by id0 View PostThen you are left with an additional step of trying to quantify the amount of Mycoplasma.
Comment
-
You can get a list of all of the available mycoplasma genomes at:
http://www.ncbi.nlm.nih.gov/genome/?term=Mycoplasma
You could combine these into a single search database and just look for hits to any parts of any of them in your screening. I don't know how complete these sequences would be in covering the diversity of mycoplasma species but if you included them all and allowed some flexibility in matching that would hopefully be fairly useful?
To do the searches we developed FastQ Screen which allows you to search through multiple databases and provides a combined report on the relative number of unique and multiple hits to each of them. It's an easy way to get quantitative or visual feedback of the amount of contamination in your libraries.
Comment
-
Originally posted by simonandrews View PostTo do the searches we developed FastQ Screen which allows you to search through multiple databases and provides a combined report on the relative number of unique and multiple hits to each of them. It's an easy way to get quantitative or visual feedback of the amount of contamination in your libraries.
Comment
Latest Articles
Collapse
-
by seqadmin
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...-
Channel: Articles
Yesterday, 07:01 AM -
-
by seqadmin
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...-
Channel: Articles
04-04-2024, 04:25 PM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, 04-11-2024, 12:08 PM
|
0 responses
57 views
0 likes
|
Last Post
by seqadmin
04-11-2024, 12:08 PM
|
||
Started by seqadmin, 04-10-2024, 10:19 PM
|
0 responses
53 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 10:19 PM
|
||
Started by seqadmin, 04-10-2024, 09:21 AM
|
0 responses
45 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 09:21 AM
|
||
Started by seqadmin, 04-04-2024, 09:00 AM
|
0 responses
55 views
0 likes
|
Last Post
by seqadmin
04-04-2024, 09:00 AM
|
Comment