User: BioRyder

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BioRyder160
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Posts by BioRyder

<prev • 51 results • page 2 of 6 • next >
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Comment: C: Canu Pacbio assembly
... In last test case, canu command failed with the following error message (job submitted with sbatch command instead of srun) -------------------- -- Starting command on Thu Mar 24 14:55:30 2016 with 256586.2 GB free disk space -- sbatch --mem=64g --cpus-per-task=16 -D `pwd` -J "meryl_date ...
written 3.4 years ago by BioRyder160
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Answer: A: miRNA Target Site prediction from unpaired data
... You can use [microRNA][1].org to see the list of miRNA target if you are having list of miRNA (Human).This application is online and does not need mRNA or UTR region to predict the miRNA target reads. [miranda][2] is an offline tool which used for miRNA target prediction.In miranda you have to prov ...
written 3.4 years ago by BioRyder160
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Comment: C: Canu Pacbio assembly
... there was no error message and program got exit. ...
written 3.4 years ago by BioRyder160
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Canu Pacbio assembly
... Hello All, I was trying to use canu assembler for pacbio read.In test case-1 I have used 3Gb data (not used HPC) and all the process, correction ,trimming & assembly, has finished in three days.When I used 30Gb data in HPC machine with SLURM , assembly process got failed after two days of run. ...
assembly written 3.4 years ago by BioRyder160 • updated 3.4 years ago by Philipp Bayer6.4k
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Comment: C: Other RNA removal from RNA-Seq Data
... Yes, this is normal procedure we do for the removal of other RNA from RNA Seq data. ...
written 3.5 years ago by BioRyder160
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Answer: A: bcl2fastq-v2 samplesheet format for dual index run
... Hello jacobnix, For dual index, Sample sheet format should be in below format .While doing bcltofastq conversion you should use the base mask as it like : -- use-bases-mask Y*,I*,I*,Y* . (Note :  each  I for Index 1 & index 2 respectively.) Sample sheet Format : [Data] Lane,Sample_ID,Sample_N ...
written 3.5 years ago by BioRyder160
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Comment: C: trimming the paired end reads with cutadapt
... Hello Ryan, Yes, you are right. they have to update their documentation.  ...
written 3.5 years ago by BioRyder160
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Comment: C: trimming the paired end reads with cutadapt
... yes, for 5' adapter you have to use -g option. ...
written 3.5 years ago by BioRyder160
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Answer: A: trimming the paired end reads with cutadapt
... Cut adapt is having only the following option. Adapter type Command-line option 3’ adapter -a ADAPTER 5’ adapter -g ADAPTER Anchored 3’ adapter -a ADAPTER$ Anchored 5’ adapter -g ^ADAPTER 5’ or 3’ (both possible) -b ADAPTER ...
written 3.5 years ago by BioRyder160
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Answer: A: Get miRNA expression from RNA-seq
... Normally miRNA read length will be 50bp including adapter.the possibility of miRNA read presence in RNA seq is all most null. Because the difference in protocols.But you can get other RNA like tRNA,rRNA from mRNA seq. ...
written 3.5 years ago by BioRyder160

Latest awards to BioRyder

Popular Question 6 months ago, created a question with more than 1,000 views. For bcl to fastq Conversion
Supporter 6 months ago, voted at least 25 times.
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: trimming the paired end reads with cutadapt
Popular Question 2.0 years ago, created a question with more than 1,000 views. For bcl2fastq-V2 base mask issue for six and eight barcode length
Popular Question 2.0 years ago, created a question with more than 1,000 views. For bcl to fastq Conversion
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Canu Pacbio assembly
Popular Question 2.0 years ago, created a question with more than 1,000 views. For base mask option in bcl to fastq conversion
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Canu Pacbio assembly
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Canu Pacbio assembly
Popular Question 2.8 years ago, created a question with more than 1,000 views. For bcl2fastq-V2 base mask issue for six and eight barcode length
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Bcl to fastq conversion problem in bcl2fastq-2.17
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: trimming the paired end reads with cutadapt
Teacher 3.3 years ago, created an answer with at least 3 up-votes. For A: trimming the paired end reads with cutadapt
Autobiographer 3.5 years ago, has more than 80 characters in the information field of the user's profile.
Scholar 3.5 years ago, created an answer that has been accepted. For A: bcl2fastq-V2 How to skip some line
Scholar 3.6 years ago, created an answer that has been accepted. For A: bcl2fastq-V2 How to skip some line

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