User: lkianmehr

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lkianmehr10
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10
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New User
Location:
France
Last seen:
6 hours ago
Joined:
5 months, 3 weeks ago
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l********@unice.fr

Posts by lkianmehr

<prev • 42 results • page 1 of 5 • next >
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how many index has to be constructed by STAR for TE analysis
... Hello, I want to make index files before map RNA-seq reads on STAR. then I need to use theses alignments as an output of TEToolkit analysis. so two annotation files mask repeated and genes are provided. for Indexing as TEToolkit manual mentioned In order to map RNA-seq reads, STAR needs an index fi ...
tetoolkit star index written 20 hours ago by lkianmehr10 • updated 20 hours ago by h.mon20k
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Comment: C: Hisat2 alignment results can be ued for TEtoolkit analysis
... I checked Hisat2 in this case and faced this sentence: HISAT2 is not designed with large values for -k in mind, and when aligning reads to long, repetitive genomes large -k can be very, very slow. ...
written 1 day ago by lkianmehr10
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Quantifying repetitive elements in RNA-seqs
... Hello, Could you please give an almost easy quantification method suggestion for repetitive elements in RNA-seq data and how can I see repetitive elements sequences for comparing between two RNA-seq reads? thanks in advance ...
quantification repetitive elements rna-seq written 1 day ago by lkianmehr10 • updated 1 day ago by Martombo2.3k
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Hisat2 alignment results can be ued for TEtoolkit analysis
... Hello, I have aligned RNA-seq reads by Hisat2, then ran TEtoolkit on sam files of Hisat2, and it works. can I trust these results? or is better to align reads again with STAR; then use TEtoolkit? ...
hisat2 tetoolkit written 4 days ago by lkianmehr10 • updated 4 days ago by h.mon20k
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Comment: C: how do Differential gene expression analysis by Salmon output
... thanks, don't you have any suggestion except tximport, because I am new in R and I can't use it, can I use aggregate option to sum genes ?" ...
written 9 days ago by lkianmehr10
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how do Differential gene expression analysis by Salmon output
... Hello, I did transcript quantification by Salmon. now I have an output like this table; Name Length EffectiveLength TPM NumReads ENSMUST00000193812.1 ENSMUSG00000102693.1 OTTMUSG00000049935.1 OTTMUST00000127109.1 RP23-271O17.1-001 RP23-271O17.1 1070 TEC 1070 885.998 12.758544 75. ...
salmon differential gene expression written 9 days ago by lkianmehr10 • updated 9 days ago by genomax57k
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how specify feature type in featureCounts
... Hello, I would appreciate if let me know how is better to specify feature type of featureCounts. actually I am not sure about that, because by default is exon, but I want to count genes and transcripts (according to 3rd column in GTF file) on sam files, so I got mixed up I have to define feature t ...
featurecounts written 17 days ago by lkianmehr10 • updated 17 days ago by Macspider2.6k
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Comment: C: how merge the gene expression value of two sample
... Sorry, I need your help to write this command correctly, because I am very new with R and DESeq2, I have written this command and faced with this problem could you please correct command it would be needed? gr <- factor(c(rep("D1", 2), rep("D3", 2))) colData <- data.frame(group=gr, ty ...
written 7 weeks ago by lkianmehr10 • updated 7 weeks ago by genomax57k
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Comment: C: how merge the gene expression value of two sample
... yes, they are technical replicates. thanks ...
written 7 weeks ago by lkianmehr10
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Comment: C: how merge the gene expression value of two sample
... No, just to know can I average them to compare them to others as one sample (D1) or not? ...
written 7 weeks ago by lkianmehr10

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