User: Sam

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Sam50
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Posts by Sam

<prev • 104 results • page 1 of 11 • next >
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retrieving long noncoding RNAs from PLANT RNA-seq
... is there any script for retrieving long noncoding RNAs from PLANT RNA-seq? Thanks in advance ...
long non coding rna written 1 day ago by Sam50
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interaction analysis of smallRNA-seq and RNA-seq data
... Dear All could you introduce me a script for interaction analysis of smallRNA-seq and RNA-seq data? means to handle RNA-seq and small RNA-seq data together for network analysis and miRNA-target interactions. Thanks ...
srnarna-se rna-seq written 1 day ago by Sam50
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Comment: C: how to annotate (rRNA, tRNA, Mt_rRNA, Mt_tRNA, etc) sequenced small RNA reads
... you can do it with local NCBI blast against Rfam (for non coding RNAs) database and then grep according to each subtype ...
written 8 days ago by Sam50
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GBS and TASSEL-GBS v2
... Dear All I'm completely new to GBS data. I have some paired-end GBS libs. can I use TASSEL-GBS v2 to handle these PE GBS libs? Thanks ...
gbs written 8 days ago by Sam50
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Comment: C: Conversion read counts to TPM for microRNAs
... TPM converting formula: TPM (transcript per million) values TPM = (miRNA total reads/total clean reads) × 1000000 ...
written 11 days ago by Sam50
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Comment: C: fastqc report for degradome reads
... I found some problem with bbmap , in bbmap output there are plenty amount of seqs with N which is mapped to genome but in bowtie2 output we don't have this problem. could you please guide me about that ? https://ibb.co/hsBte7 https://ibb.co/nsL8CS Thanks ...
written 12 days ago by Sam50
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Comment: C: fastqc report for degradome reads
... This is the company answer "Our lab is confident the mapping rate issue does not relate to any adaptor contamination, but with regard to this phenomenon you're observing, it's expected that longer, degraded RNA fragments are generally harder to map to the genome than smaller fragments." but after r ...
written 15 days ago by Sam50
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Comment: C: fastqc report for degradome reads
... as you know the issue was contaminated clean reads which provided by company and due to low mapping rate I tried to re-trim this clean reads, right now we confirm that we have a lot of artifact and adapter remanent, right ? (because company told me we are pretty sure there is not any kind of contami ...
written 15 days ago by Sam50
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Comment: C: fastqc report for degradome reads
... here is the IGV visualization, upper case is bbmap out put. https://ibb.co/c0D5Kx ...
written 15 days ago by Sam50
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Comment: C: fastqc report for degradome reads
... OK, I'II try to do that, but I have a problem with sending the post just 5 posts per 6hr, as you know I elaborate a lot on your nice website :) ...
written 18 days ago by Sam50

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Centurion 12 days ago, created 100 posts.
Rising Star 5 months ago, created 50 posts within first three months of joining.

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