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Old 12-11-2018, 11:18 PM   #1
ControlCcolon
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Location: Italy

Join Date: Dec 2018
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Default Rstudio and RNAseq

Hello Everyone,
I am a biologist and I am trying my best to learn more about RNAsequencing and in general to Rstudio. Although there are many informations online none of them was clear to me with an easy workflow to follow for processing Bam and comparing gene expressions.

I was wondering if there are online classes available,
or if any of you would like to be hired and teach me the workflow to analyse data from bam file to RPKM or FPKM matrix using Rstudio and bioconductor packages


thank you

Last edited by ControlCcolon; 12-11-2018 at 11:24 PM.
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Old 12-12-2018, 01:51 AM   #2
Wang Qing
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Location: Harbin Medical University

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Hello, I'm glad to answer for you.If you have any doubts, we can communicate further.Here is my answer.
You can use the "stringtie" in the linux.Stringtie Assembly transcripts (first convert sam files to bam files and sort them; then assemble each sample for transcripts) Put the following command under Linux.
/linuxdata1/zy/software/stringtie-1.3.4d/stringtie /linuxdata1/bxf/test/SRR3475383b.bam -o outRes.gtf -p 28 -G /linuxdata1/download/GECODE19gtf/gencode.v19.chr_patch_hapl_scaff.annotation.gtf -A gene_abund.tab -B -e;

Generate a specific file under the folder specified by -B
e2t.ctab e_data.ctab i2t.ctab i_data.ctab t_data.ctab
e is exon, i is intron, t is transcripts,e2t is the relationship between exon and transcripts, i2t is the relationship between introns and transcripts, and t_data is the data of transcripts.
-A <gene_abund.tab> File for exporting gene abundance (tab delimited format)
Note that the sorted bam files should be placed,-o is the output result file, which contains RPKM and TPM values.-G is the gene annotation file downloaded by genecode.
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Old 04-10-2019, 10:38 PM   #3
gradymay
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Location: NY

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Quote:
Originally Posted by Wang Qing View Post
Hello, I'm glad to answer for you.google street view If you have any doubts, we can communicate further.Here is my answer.
You can use the "stringtie" in the linux.Stringtie Assembly transcripts (first convert sam files to bam files and sort them; then assemble each sample for transcripts) Put the following command under Linux.
Great! Thank you very much
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