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Old 05-24-2016, 10:06 PM   #1
lufeng891109
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Default Trinity assembly and mapped reads is 0.2%

HI,All:
I used trinity to assembly my rna data to get isoforms with the combined way.then maped my data to the sequence by the RSEM,but mapped read of one sample is 0.2% ;Trinity and RSEM ran successfully.Then I rebuided my sample library and resequenced the sample .Lucky the mapped read is more than 70%.
Now i meet the question again ,I donot get the reason.Anybody can help me ?Thanks
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Old 05-25-2016, 06:11 AM   #2
jordi
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Which commands did you use with Trinity and RSEM?
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Old 05-25-2016, 11:56 AM   #3
kmcarr
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Quote:
Originally Posted by lufeng891109 View Post
HI,All:
I used trinity to assembly my rna data to get isoforms with the combined way.then maped my data to the sequence by the RSEM,but mapped read of one sample is 0.2% ;Trinity and RSEM ran successfully.Then I rebuided my sample library and resequenced the sample .Lucky the mapped read is more than 70%.
Now i meet the question again ,I donot get the reason.Anybody can help me ?Thanks
Most likely answer seems to me that the original library which did not map wasn't what you thought it was. It could be that somewhere along the line in sample isolation, transfer, library construction, etc the sample either became contaminated or mixed up.

Did you try taking a sample of reads from that library and BLASTing them against NCBI nt database to see what species they most closely match? Is it the species it was supposed to be?
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Old 05-25-2016, 09:24 PM   #4
lufeng891109
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Quote:
Originally Posted by jordi View Post
Which commands did you use with Trinity and RSEM?
thanks jordi . The commands are;
1:--seqType fq --JM 50G --CPU 5 --min_contig_length 200 --group_pairs_distance 500 --left read1.fq --right left2.fq --min_kmer_cov 1 --bflyHeapSpaceMax 20G --output /home/xugl/test/maize/Analysis/Basic_Analysis/Assembly/Trinity_assembly/All_Combination/All_Combination_Trinity --no_cleanup --bflyGCThreads 5
2erl run_RSEM_align_n_estimate.pl --transcripts Trinity.fasta --left read1.fq --right read2.fq --seqType fq --prefix T1
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Old 05-25-2016, 09:32 PM   #5
lufeng891109
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Originally Posted by kmcarr View Post
Most likely answer seems to me that the original library which did not map wasn't what you thought it was. It could be that somewhere along the line in sample isolation, transfer, library construction, etc the sample either became contaminated or mixed up.

Did you try taking a sample of reads from that library and BLASTing them against NCBI nt database to see what species they most closely match? Is it the species it was supposed to be?
Thanks kmcarr。
I did blasting with nt and get no contaminations 。I am sure that the samples were not mixed up.

Last edited by lufeng891109; 05-26-2016 at 09:01 PM.
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