User: Amaranta Remedios

Reputation:
10
Status:
New User
Location:
Manchester
Last seen:
1 week, 5 days ago
Joined:
11 months, 4 weeks ago
Email:
l*********************@postgrad.manchester.ac.uk

Posts by Amaranta Remedios

<prev • 13 results • page 1 of 2 • next >
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Comment: C: Help with for loop for sequence alignment using STAR
... I corrected that, I can see how that would be confusing. Thanks, It really is a STAR index ...
written 5 weeks ago by Amaranta Remedios10
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Help with for loop for sequence alignment using STAR
... Hi, I am trying to run a sequence alignment with STAR. I have a total of 28 files paired-end files, 14 R1 and 14 R2. My files are called like this: mapped_trimmed.LLC7b_Aligned.sortedByCoord.out.bam_R2.fq mapped_trimmed.LLC7a_Aligned.sortedByCoord.out.bam_R2.fq mapped_trimmed.LLC1b_Ali ...
star unix written 5 weeks ago by Amaranta Remedios10
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Statistical test for target enrichment for each microRNA
... Hi, I have this conceptual question that I have been struggling with for a while due to my poor knowledge of statistics. I hope someone can help me to identify the correct test. I have a list of microRNAs in a specie, and I have predicted the targets for each microRNAs. I have also done differen ...
target enrichement micrornas statistics written 3 months ago by Amaranta Remedios10
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Comment: C: Build consensus sequences from repeat masker output
... Thanks for the comment. I have already extracted the fasta sequences. I guess the way to move forward would be to do some sort of clustering on the sequences but I am not just sure about that. ...
written 8 months ago by Amaranta Remedios10
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Build consensus sequences from repeat masker output
... Hi, So I have a repeat masker output file for a new organism (crustacean). And I want to use the transposable elements in this specie to analyse the piRNAs (using my own sequencing data=short reads). The problem is I would like to get **consensus sequences for transposable elements** in this spe ...
transposable elements repeatmasker written 8 months ago by Amaranta Remedios10 • updated 5 months ago by bioinfo0
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Comment: C: Where do I find viral genomes that can attack a particular phylum
... Thanks, very cool and useful feature !! ...
written 9 months ago by Amaranta Remedios10
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Where do I find viral genomes that can attack a particular phylum
... I work with a model crustacean organism and I would like to find some sort of database where I can first find viruses that would attack arthropods or crustaceans and then get their genomes. I was wondering if such thing exist or if I have to do the research independently myself which will take time ...
crustaceans genomes databases virus written 9 months ago by Amaranta Remedios10
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Comment: C: Error python script overlapping_reads.py
... Thanks a lot ! It was exactly that. What solved it was to add this to my script: `#!/Users/user/.pyenv/shims/Python` and run with python2.7 ...
written 9 months ago by Amaranta Remedios10
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Error python script overlapping_reads.py
... Hi, I am trying to run this script overlapping_reads.py https://github.com/ARTbio/tools-artbio/blob/master/tools/small_rna_signatures/overlapping_reads.py However I keep getting this error and I don't really know how to solve it. Any suggestion? samtools index sorted_g.mapped_TEs_new_f.bam &a ...
python github script written 9 months ago by Amaranta Remedios10
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Comment: C: bash bowtie script output with prefix
... Because I will loop again and that makes it easier to recognise just the new files in that folder. Thanks ! ...
written 9 months ago by Amaranta Remedios10

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