User: Buffo

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Buffo1.2k
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Posts by Buffo

<prev • 249 results • page 1 of 25 • next >
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Comment: C: miRNA seq suggested read count and applicability on Illumina iSeq 100
... Keeping in mind that there is no method to sequence just miRNAs and exclude other kind of short RNAs, if you consider 20M too high for human... go ahead, personally I do not think so. ...
written 2 days ago by Buffo1.2k
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Comment: C: miRNA seq suggested read count and applicability on Illumina iSeq 100
... It depends of your specie of interest and expected miRNAs to calculate the coverage needed. And also of what you want to analyze, , for example, to analyze expression (in mouse) 20M would be enough, However, to distinguish between isomirs and/or look for new probable miRNAs you will need more cover ...
written 2 days ago by Buffo1.2k
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Comment: C: miRNA alignment using bowtie 2
... Since your high alignment rate may be no surprinsing, you would check if your reads really correspond to miRNAs, short RNA is not a miRNA by default, but also I recommend you to perform ungapped alingnments with bowtie2 or use Bowtie(1) to avoid isomirs. ...
written 4 days ago by Buffo1.2k
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Comment: C: Circular Genome Alignment
... bwa has the option to apply soft and hard clipping, it may be usefull, or hisat2 by default performs spliced alignments. ...
written 9 days ago by Buffo1.2k
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Answer: A: Tools to predict microRNAs in Ascomycota(Fungus)
... [mirDeep][1] works fine, but do not use it until you have read and understand the manual and protocol to predict new miRNAs. Small RNAs are not miRNAs by default. [1]: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3553977/ ...
written 17 days ago by Buffo1.2k
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Comment: C: Remove specific number of identical reads from fastq or bam files
... [prinseq][1] can remove duplicated sequences. If you have a high levels of read-duplication you may consider to remove them, if not, I think that use arbitrary filters may cause absolutely biased analysis. [1]: http://prinseq.sourceforge.net/manual.html ...
written 18 days ago by Buffo1.2k
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Comment: C: Aligning miRNA reads to miRbase
... $cat hairpin.fa mature.fa > both.fa ...
written 7 weeks ago by Buffo1.2k
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Comment: C: Aligning miRNA reads to miRbase
... I recommend you to use both, mature and hairpin because you may found new miRNA variants or "isoforms". And also, recommend you to use bowtie (no bowtie2 or blast) to align them, it is easy to handle and filter multihits. ...
written 7 weeks ago by Buffo1.2k
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Comment: C: Hide insertion sites in IGV Browser, is it possible?
... Thanks Pierre :D, exactly what I cant see in front my eyes. ...
written 8 weeks ago by Buffo1.2k
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Hide insertion sites in IGV Browser, is it possible?
... Hi, By default IGV indicates insertions with respect to the reference with a purple I, and I would like to hide it or change the color, I have read the manual and it is making me crazy, I can´t find the way to do it, somebody knows if it is possible? ...
alignment igv written 8 weeks ago by Buffo1.2k

Latest awards to Buffo

Commentator 6 weeks ago, created a comment with at least 3 up-votes. For A: GO analysis of Soybean
Popular Question 6 weeks ago, created a question with more than 1,000 views. For Pipeline for genome annotation?
Popular Question 11 weeks ago, created a question with more than 1,000 views. For Pipeline for genome annotation?
Popular Question 3 months ago, created a question with more than 1,000 views. For Pipeline for genome annotation?
Popular Question 3 months ago, created a question with more than 1,000 views. For piRNA target-interaction database?
Popular Question 3 months ago, created a question with more than 1,000 views. For piRNA target-interaction database?
Popular Question 5 months ago, created a question with more than 1,000 views. For piRNA target-interaction database?
Guru 7 months ago, received more than 100 upvotes.
Scholar 7 months ago, created an answer that has been accepted. For A: How can I get FASTA if i have Names of proteins ?
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: How can I get FASTA if i have Names of proteins ?
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: How to convert GTF to gff file for read count using HTSeq
Scholar 8 months ago, created an answer that has been accepted. For A: How can I get FASTA if i have Names of proteins ?
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: How can I get FASTA if i have Names of proteins ?
Popular Question 11 months ago, created a question with more than 1,000 views. For Genomic assembly with spades
Supporter 15 months ago, voted at least 25 times.
Scholar 18 months ago, created an answer that has been accepted. For A: How can I get FASTA if i have Names of proteins ?
Centurion 19 months ago, created 100 posts.
Scholar 22 months ago, created an answer that has been accepted. For A: How can I get FASTA if i have Names of proteins ?
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: How can I get FASTA if i have Names of proteins ?

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