User: wasphunter

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wasphunter0
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Posts by wasphunter

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Comment: C: Extreme normalization using Trinity related to poor mapping efficiency?
... I only did the FastQC analysis reported above in BACKGROUND. I found evidence for adapter contamination but was readily able to remove that using Trimmomatic. What else would you recommend? ...
written 5 months ago by wasphunter0
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Extreme normalization using Trinity related to poor mapping efficiency?
... Hello. QUESTION: Can the combination of high levels of pre-mRNA and extreme normalization explain a poor mapping rate? ISSUE: I am getting poor mapping efficiency (~64%) from my RNAseq reads against a Trinity assembly derived from a normalized subset of those reads. There is little evidence of DNA ...
mapping efficiency normalization rna-seq written 6 months ago by wasphunter0 • updated 4 months ago by Biostar ♦♦ 20
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Comment: C: fastQC - case of the anomalous last base
... Thanks for your comments, James. I used Trimmomatic for the adapter removal in both single and palindromic modes. I'm not sure which software was used to remove the index adapters (still checking with my sequencing company). The data came to me with almost all reads 125 bases in length. The fa ...
written 6 months ago by wasphunter0
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Comment: C: fastQC - case of the anomalous last base
... Thank you for your input. My RNAseq data derives from 125 bp paired-end reads. I should have stated more clearly that the "errant" bases are at the 3' end of the reads, not the 5'. Apologies for not including an image earlier: [content across all bases][1] I believe I did a good job of remo ...
written 6 months ago by wasphunter0
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fastQC - case of the anomalous last base
... Hello. I am not getting the best mapping rate (~60%) on my latest batch of sequence from a HiSeq run following de novo assembly. I don't see a lot of evidence for DNA contamination in the reads so I've been looking elsewhere for a reason for the low mapping efficiency. My sequences appear to hav ...
rna-seq fastqc written 6 months ago by wasphunter0 • updated 6 months ago by Grinch0
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Comment: C: Trinity - in silico normalization before/after trimmomatic?
... Thanks Farbod. I was aware of the capacity to package all steps in a single Trinity run. That is attractive but, like many, I have limited access to computing resources. It seemed to me prudent to create a high-quality, normalized data set one time that I could then use for any downstream assemblie ...
written 8 months ago by wasphunter0
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Comment: C: Trinity - in silico normalization before/after trimmomatic?
... Thanks for the advice and links, Brian. I've been considering BBNorm for all the reasons you mention in support of the software above and elsewhere. ...
written 8 months ago by wasphunter0
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Trinity - in silico normalization before/after trimmomatic?
... I have 100+ million paired-end reads from which adapter sequences have been removed but quality trimming has not yet been conducted. It seems most efficient from a memory utilization standpoint to conduct in silico normalization and trimmomatic steps FIRST and only once and then to use normalized/tr ...
rna-seq written 8 months ago by wasphunter0 • updated 8 months ago by Farbod3.0k

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