User: lkianmehr
lkianmehr • 10
- Reputation:
- 10
- Status:
- New User
- Location:
- France
- Last seen:
- 6 hours ago
- Joined:
- 5 months, 3 weeks ago
- Email:
- l********@unice.fr
Posts by lkianmehr
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... 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 ...
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... 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
lkianmehr • 10
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... 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
...
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... 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? ...
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... 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
lkianmehr • 10
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... 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. ...
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... 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 ...
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... 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 ...
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232
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... yes, they are technical replicates. thanks ...
written 7 weeks ago by
lkianmehr • 10
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... No, just to know can I average them to compare them to others as one sample (D1) or not? ...
written 7 weeks ago by
lkianmehr • 10
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