Question: low percentage mapping... tophat2.1.1
0
gravatar for mra8187
19 months ago by
mra818720
mra818720 wrote:

hi im working on RNA-seq data of honey bee apis.mellifera.mellifera for trim the data i am using trimmomatic and it is the resaults :

single end https://www.dropbox.com/s/wqqxav4qxy3sk1e/single-end.zip?dl=0

paired end1 https://www.dropbox.com/s/b7rfgqgee3ds9u3/SRR1571716-1.trimmed_fastqc.zip?dl=0

paired end2 https://www.dropbox.com/s/5zqc4sgg3ccrtcr/SRR1571716-2.trimmed_fastqc.zip?dl=0

because reverse has bad quality im using forward only (single) and script tophat2.1.1:

single : tophat2 -p 4 -G anotation.gtf -o output indexed-refrence.fa trimmed1.fastq.gz

paired : tophat2 -p 4 -r 200 --mate-std-dev 50 -G anotation.gtf -o output indexed-refrence.fa trimmed1.fastq.gz trimmed2.fastq.gz

and tophat output:

single : Reads: Input : 10858264 Mapped : 4083998 (37.6% of input) of these: 53299 ( 1.3%) have multiple alignments (16 have >20) 37.6% overall read mapping rate.

paired : Left reads: Input : 8066646 Mapped : 3376613 (41.9% of input) of these: 41967 ( 1.2%) have multiple alignments (61 have >20) Right reads: Input : 8066646 Mapped : 4488196 (55.6% of input) of these: 55841 ( 1.2%) have multiple alignments (66 have >20) 48.7% overall read mapping rate.

Aligned pairs: 3164464 of these: 39807 ( 1.3%) have multiple alignments 9497 ( 0.3%) are discordant alignments 39.1% concordant pair alignment rate.

why mapping is so low in each condition ?

snp rna-seq next-gen • 751 views
ADD COMMENTlink written 19 months ago by mra818720
2

Any time you start seeing low alignments, the first thing to do is to take a set of reads that are not aligning and blast them at NCBI to make sure there is no issue with data (e.g. contamination).

ADD REPLYlink written 19 months ago by genomax49k

thank you for your advise ...

ADD REPLYlink written 19 months ago by mra818720
1

may I ask why you do not use HISAT2?

ADD REPLYlink written 19 months ago by Medhat7.6k

thank you for your advise ...

ADD REPLYlink written 19 months ago by mra818720
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