User: prp291

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prp29150
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Posts by prp291

<prev • 36 results • page 1 of 4 • next >
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Answer: A: Has anyone run Phobius locally? Error - could not read provided fasta sequences
... Just for future visitors, My fasta file was with "*" at the end of every sequence and I was getting the same error i.e. 'could not read provided fasta file'. I remove the "*" and run the Phobius without any other change and it finished successfully. ...
written 3 months ago by prp29150
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Comment: C: Proovread terminated with error
... Sorry. I used 17 million reads from a non-model plant. I have 70 GB with 8 threads. ...
written 4 months ago by prp29150
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Comment: C: Proovread terminated with error
... Thanks for the comment. My command looks like this perl proove/proovread/bin/proovread -l Lang_flnc.fasta.CDHIT.fasta -s normalized.fastq -o re I have enough memory too. ...
written 4 months ago by prp29150
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Proovread terminated with error
... I run proovread with following command perl proove/proovread/bin/proovread -l Lang_flnc.fasta.CDHIT.fasta -s normalized.fastq -o re After running for 5 days, it terminated with the following error. Reading normalized.fastq Killed [E::sam_parse1] incomplete aux field [W::s ...
proovread bwa written 4 months ago by prp29150
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Comment: C: Combining the RNAseq datasets
... actually I want to identify the tissue specific genes in my plants. 100bp and 50bp datasets cover different kind of tissue. So my goal is to mixed of both datasets and then identify the tissue specific genes. Thanks. ...
written 2.3 years ago by prp29150
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Comment: C: Combining the RNAseq datasets
... Thanks for comments. I am using a plant genome. Both 50bp and 100bp showed more than 70 % alignment rate. ...
written 2.3 years ago by prp29150
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Comment: C: Combining the RNAseq datasets
... I think this answer was not intended for this question. ...
written 2.3 years ago by prp29150
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Comment: C: Combining the RNAseq datasets
... Thanks for the links. I think situation is little bit different in my case. In my case both datasets are using the technique (RNAseq) but read length is different. I was wondering whether difference in read length will me any impact on final result? ...
written 2.4 years ago by prp29150
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Combining the RNAseq datasets
... I have a RNAseq experiment data (50bp) into two tissue. I want to combine it with previously reported RNAseq data (100bp) to analyze the gene expression in different tissue. Can I combine both data together or I should go through some kind of normalization? Any insight will be helpful. Thanks ...
next-gen rna-seq written 2.4 years ago by prp29150 • updated 2.3 years ago by theobroma221.1k
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Plant pathogen interaction RNAseq analysis
... Hi, Yesterday I [post a question][1] about different mapping percentage for control and treated (virus infected) plant. Later I found that about 25% of my reads from treated libraries are mapping with the virus genome I used for infection that leads the discrepancy in mapping rate. My question is ho ...
rna-seq written 3.3 years ago by prp29150

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Popular Question 9 weeks ago, created a question with more than 1,000 views. For Reference sequence for miRna expression analysis
Popular Question 4 months ago, created a question with more than 1,000 views. For Data format to produces a heatmap like this
Popular Question 18 months ago, created a question with more than 1,000 views. For Data format to produces a heatmap like this
Popular Question 18 months ago, created a question with more than 1,000 views. For Bowtie2 low mapping percentage
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Bowtie2 low mapping percentage
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Get specific elements from clustered data in R
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Bowtie2 low mapping percentage
Great Question 3.0 years ago, created a question with more than 5,000 views. For Extract Fasta Sequences Sub Sets
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Bowtie2 low mapping percentage
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Eukaryotic genome annotation steps
Popular Question 3.7 years ago, created a question with more than 1,000 views. For Extract Fasta Sequences Sub Sets
Popular Question 5.5 years ago, created a question with more than 1,000 views. For Extract Fasta Sequences Sub Sets

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