User: Nelislam4

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Nelislam420
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Posts by Nelislam4

<prev • 12 results • page 1 of 2 • next >
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Comment: C: Visualizing alternative splicing events
... Thanks for your response, actually the link requires login domain as certificate. Did you means avg PSI values which is in .clustvec file? Thanks, Nour ...
written 26 days ago by Nelislam420
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Visualizing alternative splicing events
... Dears, I have TPM read counts of RNA-seq data from Salmon, then I have used SUPPA2 for alternative splicing events detection. The point is, I need a tool to visualize the alternative splicing events across conditions? and what files should I consider for these visualization, TPM read counts or psi ...
rna-seq written 26 days ago by Nelislam420
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Detection of Novel splice events
... Hi, I have .bam files aligned by hisat2 using genome FASTA file as the reference, after that I made up my mind to use SUPPA2 for the detection of **Novel splice variants** which recommends Salmon for transcript quantifications due to their TPM values, however, salmon uses the transcriptomic.fasta as ...
alignment rna-seq written 5 weeks ago by Nelislam420
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Comment: C: DEseq2 design with multiple assays, conditions, and replicates
... What did you mean by combo column! ....**assays** column? Thanks, ...
written 7 weeks ago by Nelislam420
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Comment: C: Deseq2 more than two condition
... Many Thanks for your response and support. Regarding to your first answer, I think that I didn't need condition column to be add in design, I just need salt environment without hours which is represented by **salt.3**. However, I have another question as well, Should I change the names of cold varia ...
written 7 weeks ago by Nelislam420
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Deseq2 more than two condition
... Hi, I am stuck in differential gene expression analysis (more than two condition) with Deseq2, here is the colData table: Sample.Type env condition WT cold cold.3 WT cold cold.3 WT cold cold.6 WT cold cold.6 WT cont cont.3 WT cont cont.3 WT cont cont.6 WT cont c ...
rna-seq written 7 weeks ago by Nelislam420 • updated 7 weeks ago by swbarnes29.2k
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(Closed) indication of N's sequences in reference genome
... Hi, I just wanna know. What is the function of N's sequences in any reference genome? What is the indication of them in the reference genome? When I've searched about it in the README file of Human Reference Genome of Ensembl, I found that it's masked sequences because they are repeats in the gen ...
genome assembly written 7 months ago by Nelislam420
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Comment: C: Transcriptomic assembly Stringtie
... Thanks for your kind response, merging bam files prior to stringtie solve the issue of merging gtf files from each bam file; however, the coverage still an issue cos there will be replicates from the same sample......so How can I solve this problem?? ...
written 13 months ago by Nelislam420
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Transcriptomic assembly Stringtie
... Hi, I have replicates of RNA-seq sample from the same sample but on different lanes, and I need to run transcriptomic assembly by Stringtie so I have run their tutorial and merge the gtf files from every sample of replicates by StringTie --merge into a single gtf file that has the complete transcri ...
assembly stringtie rna-seq written 14 months ago by Nelislam420 • updated 14 months ago by ATpoint42k
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Comment: C: Mark duplicate "Picard"
... Thanks for your help ...
written 14 months ago by Nelislam420

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