User: rahmati.razieh83

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Posts by rahmati.razieh83

<prev • 26 results • page 2 of 3 • next >
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Comment: C: mapping and quantification of paired end reads using BBmap
... Dear ahmad; Thanks alot for your comment. I have already trimmed universal adapters by trimmomatic. But I found out, in addition to adapters my reads contains some random Lexogen primers. because of existing these primers, I have been recommended to use bbmap instead of top hat2 for mapping the read ...
written 2.6 years ago by rahmati.razieh8330
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Comment: C: trimming PE RNA Reads
... before assembly I trimmed adapters but not Lexogen primers. So I think this assembly contains Lexogen primers ...
written 2.6 years ago by rahmati.razieh8330
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Comment: C: trimming PE RNA Reads
... thanks a lot for your comment. According to what you recommended me, I decided to keep Lxogen primer but use bbmap instead of Tophat2 to map the reads. I assembled paired end reads with trinity and now I have a trinity.fasta file. for the next step I need to map paired end reads to de novo assembl ...
written 2.6 years ago by rahmati.razieh8330
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mapping and quantification of paired end reads using BBmap
... Hi everyone I have some paired end RNA -seq reads without reference genome. I assembled them by using trinity. because my reads containing specific Lexogen primers, I have been recommended to use bbmap instead of Tophat2 in order to avoid map rate decrease. I assembled the reads with trinity and ...
rna-seq written 2.6 years ago by rahmati.razieh8330 • updated 2.6 years ago by ahmad mousavi480
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Comment: C: setting CPU and max memory for running trinity
... I edited my post and attached the error file. ...
written 2.6 years ago by rahmati.razieh8330
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Comment: A: setting CPU and max memory for running trinity
... This is the error I have received ![enter image description here][1] [1]: http://uupload.ir/files/4xa_trinityerror.png ...
written 2.6 years ago by rahmati.razieh8330
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Comment: A: setting CPU and max memory for running trinity
... according to my running command and the error I received, what is the problem? Does it need to I change the settings in command? ...
written 2.6 years ago by rahmati.razieh8330
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setting CPU and max memory for running trinity
... ![enter image description here][1]Hi everyone I run Trinity with this command cd $HOME module load bowtie2 SAMTools-1.4.1 Trinity-2.4.0 Trinity --seqType fq --left all.left.trimmed2.fq --right all.right.trimmed2.fq --CPU 40 --max_memory 40G --bflyCPU 30 --monitoring --bflyCalculateCPU > $HOME/ ...
rna-seq written 2.6 years ago by rahmati.razieh8330
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Comment: C: using BBmap to map paire end reads to de-novo assembled transcriptome
... Thank you so much for your comment ...
written 2.6 years ago by rahmati.razieh8330
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using BBmap to map paire end reads to de-novo assembled transcriptome
... Dear all I received some RNA seq reads containing Lexogen primers. My reads do not have any refrence genome. Because of existing primers in the reads, mapping my reads by TopHat to assembled transcriptome will reduce the mapping rate significantly. Regarding having no reference genome, Can I map m ...
rna-seq written 2.6 years ago by rahmati.razieh8330 • updated 2.6 years ago by genomax85k

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