I do primarily single ended reads, but for alignment quality I look primarily at
1) pct of reads mapped
2) pct of reads uniquely mapped
It sounds like you are also asking about post-alignment qc in general and I add
3) read duplication (ie how many reads align to identical location) - most reads should have only one or several.
4) reads biotype distribution (most should map to protein-coding regions)
5) cumulative pct measures - I sort genes by count or fpkm and graph # of genes vs cumulative percentage. That will tell you if you are sinking a lot of reads into very common transcripts and tell you that you might need more depth to see certain less common transcripts.
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
How about proportion of duplicate fragments? This will depend on whether you've done single- or paired-end reads, though, since with single RNA-seq reads you do expect a certain amount of duplication by chance (with paired reads it's a much smaller chance).
Leave a comment:
-
Originally posted by maxsalm View PostFastQC may also be of general use: http://www.bioinformatics.babraham.a...ojects/fastqc/
Leave a comment:
-
FastQC may also be of general use: http://www.bioinformatics.babraham.a...ojects/fastqc/
Leave a comment:
-
Also take a look at RSeQC: http://rseqc.sourceforge.net/
Most aligners will produce stats on alignments e.g. BBMap, TopHat and probably STAR as well.
Leave a comment:
-
hi Dan,
Have a look at "samtools flagstat"
The output will looks something like this and I think it contains all the info you requested.
Code:7276199 + 0 in total (QC-passed reads + QC-failed reads) 0 + 0 duplicates 7276199 + 0 mapped (100.00%:-nan%) 7276199 + 0 paired in sequencing 3787000 + 0 read1 3489199 + 0 read2 6195536 + 0 properly paired (85.15%:-nan%) 6795026 + 0 with itself and mate mapped 481173 + 0 singletons (6.61%:-nan%) 480036 + 0 with mate mapped to a different chr 480036 + 0 with mate mapped to a different chr (mapQ>=5)
Leave a comment:
-
FASTQ alignment metrics (RNA-Seq)?
Hello,
How do people judge the quality of a FASTQ (short read) alignment? In particular I'm interested in evaluating RNA-Seq alignments, typically (but not exclusively) from ILLUMINA instruments.
What comes to mind is:
* Fraction of reads mapped
* Fraction of reads mapped uniquely
* Fraction of 'good' pairs (right orientation, right distance)
and for RNA-Seq specifically
* Fraction of reads mapping within a gene
Anything based on read mapping quality?
What other metrics can we think of?Tags: None
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
04-22-2024, 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, Yesterday, 11:49 AM
|
0 responses
15 views
0 likes
|
Last Post
by seqadmin
Yesterday, 11:49 AM
|
||
Started by seqadmin, 04-24-2024, 08:47 AM
|
0 responses
16 views
0 likes
|
Last Post
by seqadmin
04-24-2024, 08:47 AM
|
||
Started by seqadmin, 04-11-2024, 12:08 PM
|
0 responses
61 views
0 likes
|
Last Post
by seqadmin
04-11-2024, 12:08 PM
|
||
Started by seqadmin, 04-10-2024, 10:19 PM
|
0 responses
60 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 10:19 PM
|
Leave a comment: