User: nidhi.vijayan13

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Posts by nidhi.vijayan13

<prev • 10 results • page 1 of 1 • next >
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Comparing Sample replicates with PtR (Trinity). Are they normalized?
... So I have 9 replicates for one sample. When I applied PtR --compare_replicates and --log2 --CPM --prin_comp 3 on them, 6 clustered together and 3 clustered differently. I got similar differentiation using --sample_cor_matrix. However, these samples are not normalized right? The 3 samples that clust ...
trinity rna-seq written 8 months ago by nidhi.vijayan1320 • updated 7 months ago by Biostar ♦♦ 20
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Why does the transcriptome from squid sp U. aligns only 1% with squid sp. E genome?
... I downloaded the transcriptome from a published paper where they sequenced the transcriptome from different organs of 2 different species of squid (squid U and squid E). Our lab recently sequenced the whole genome of Squid E. When I aligned the transcriptome of squid E from the previously published ...
rna-seq written 9 months ago by nidhi.vijayan1320
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Answer: A: Trinity run_DE_analysis samples.txt file format?
... I got help and rectified it. I re-made the samples file in the terminal with command line, then it worked. Creating tab delimited text from excel, is not compatible for some scripts. ...
written 9 months ago by nidhi.vijayan1320
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Trinity run_DE_analysis samples.txt file format?
... Its not running the analysis. I think there is something wrong with my samples file, but I used it fine to compare replicates with PtR. what is the samples versus data fields? My script: /trinityrnaseq-v2.8.6/Analysis/DifferentialExpression/run_DE_analysis.pl --matrix Trinity_kallisto.isoform.c ...
trinity rna-seq written 9 months ago by nidhi.vijayan1320
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Answer: C: Bowtie2 error RNA seq aligning to genome
... I fixed it by using the following script: java -jar $Trimmomatic PE ~/transcriptome/WT_LO2_1.fastq ~/transcriptome/WT_LO2_2.fastq LO2_forward_paired.fq.gz LO2_forward_unpaired.fq.gz LO2_reverse_paired.fq.gz LO2_reverse_unpaired.fq.gz ILLUMINACLIP:TruSeq3-PE:2:30:10:2:TRUE LEADING:3 TRAILING:3 SLIDI ...
written 10 months ago by nidhi.vijayan1320
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Bowtie2 error RNA seq aligning to genome
... I first used Trimmomatic using the command: java -jar $Trimmomatic PE ~/transcriptome/WT_LO2_1.fastq ~/transcriptome/WT_LO2_2.fastq ~/transcriptome/trimmed/WT_LO/WT_LO2_forward.fq.gz ~/transcriptome/trimmed/WT_LO/WT_LO2_reverse.fq.gz ILLUMINACLIP:TruSeq3-PE:2:30:10 LEADING:3 TRAILING:3 SLIDING ...
assembly alignment rna-seq written 10 months ago by nidhi.vijayan1320 • updated 10 months ago by genomax89k
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Comment: A: Trimmomatic: Higher number of "forward only" than "reverse only" surviving reads
... I am having the same issue. But when I align to the genome using bowtie2, I get an error: Error, fewer reads in file specified with -2 than in file specified with -1 terminate called after throwing an instance of 'int' (ERR): bowtie2-align died with signal 6 (ABRT) ...
written 10 months ago by nidhi.vijayan1320
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Comment: C: Transcripts highly constitutively expressed
... Thanks for all the suggestions! Will try the p-value, log fold change and replicating with published results. If anyone is familiar with a good paper that does something similar and share it, I would really appreciate it! THANKS much ...
written 10 months ago by nidhi.vijayan1320
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Transcripts highly constitutively expressed
... How do I identify transcripts that are NOT differentially expressed? I have RNA-seq data that I have assembled using trinity. I want to see which transcripts are highly expressed in all replicates and between 2 different types of tissues. ...
rna-seq written 10 months ago by nidhi.vijayan1320 • updated 10 months ago by ATpoint38k
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Forum: Are OTUs an accurate measure of abundance?
... I am having a debate with my PI when interpreting the information provided by the OTU table. The question is, is the OTU table generated after sequence alignments with database provide accurate information for estimating the number of bacteria present in that sample? For example if we have OTU10 wh ...
16s rrna next-gen forum written 2.7 years ago by nidhi.vijayan1320 • updated 2.7 years ago by grp200940

Latest awards to nidhi.vijayan13

Scholar 10 months ago, created an answer that has been accepted. For C: Bowtie2 error RNA seq aligning to genome
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Are OTUs an accurate measure of abundance?

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