Terrible RNA mapping result by STAR
Hi，all It was the first time for me to map RNA sequence. The data generated from corals .I used STAR to map the sequence to the reference. I used the default parameter but got a terrible result. The final mapping result was
Started job on | Dec 12 16:02:44
Started mapping on | Dec 12 16:03:13
Finished on | Dec 12 16:12:34
Mapping speed, Million of reads per hour | 85.99
Number of input reads | 13400813
Average input read length | 150
UNIQUE READS:
Uniquely mapped reads number | 3114
Uniquely mapped reads % | 0.02%
Average mapped length | 124.34
Number of splices: Total | 41
Number of splices: Annotated (sjdb) | 2
Number of splices: GT/AG | 24
Number of splices: GC/AG | 4
Number of splices: AT/AC | 0
Number of splices: Non-canonical | 13
Mismatch rate per base, % | 4.13%
Deletion rate per base | 0.03%
Deletion average length | 1.86
Insertion rate per base | 0.01%
Insertion average length | 1.47
MULTI-MAPPING READS:
Number of reads mapped to multiple loci | 1505
% of reads mapped to multiple loci | 0.01%
Number of reads mapped to too many loci | 47
% of reads mapped to too many loci | 0.00%
UNMAPPED READS:
% of reads unmapped: too many mismatches | 0.00%
% of reads unmapped: too short | 99.96%
% of reads unmapped: other | 0.00%
CHIMERIC READS:
Number of chimeric reads | 0
% of chimeric reads | 0.00%
Is there any idea about the too many unmapped reads? I didn't understand what the reason 'too short' mean. Can somebody explain it？Thanks!
• 2,499 views
•
link
written
by
610225668 •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Decent Uniquely mapped reads but no features
written by ju_ra •
-
trouble with 'too short' reads using STAR. each mate maps fine, but the paired end mapping does not
written by james.alan.gregory •
-
Mapping reads to combined mouse and human genome
written by fifty_fifty •
-
question about the equation of counts in STAR ReadsPerGene.out.tab
written by boymin2020 •
-
STAR mapping results
written by mxlsherry1992 •
-
Empty BAM file upon mapping with STAR
written by makwana.kd •
-
the lower unique mapping rate after Trimming
written by lilingjoyo •
-
STAR outputs interpretation
written by XBria
-
high % of reads mapped to multiple loci after STAR mapping
written by Lila M
-
Recommended doc for interpreting STAR alignment stats
written by emblake •
Too short means too short alignment. Are you sure you use the right reference?
In fact, I have nine types of coral,and I chosen five of these to build the reference index independently.But unfortunately, the results were similar
Can you elaborate on this ? Are you just using short contigs as a reference (please give stats, like using bbmaps stats.sh) ? Are you aligning against a single species ?
Have you tried bwa-mem or minimap2 to check their mapping rates for general info ? Have you ever tried alignments to these references before ?
Could you send your data to a pre-processing software like fastqc
What are your reads length ?
What is you command line to align ?
% of reads unmapped: too shortcan mean two things with STAR :I've notice that older STAR versions have issues with PE-reads having too much of an overlap.
If you've got PE data, try only R1 first. Otherwise, check your FastQC reports, as Batien mentioned, for adapter-contamination or overrepresented sequences indicating other contaminations.