User: morteza.aslanzadeh

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Posts by morteza.aslanzadeh

<prev • 11 results • page 1 of 2 • next >
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Samtools flagstat with sncRNA (single-end reads)
... Hi, I am analyzing sncRNA reads (single-end) provided by ```Nextflex``` sequencing method. I used ```bowtie``` with ```-m 1``` option to align the reads to the mouse genome. Then I used ```HTSeq-count``` to count the number of reads assign to each feature. I get low counts in ```HTSeq-count``` and ...
sequence alignment rna-seq written 21 hours ago by morteza.aslanzadeh10
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Comment: C: How many of the reads end up being counted by HTSeq count
... Thank you, Tamir for the answer. So after removing that extra lines, should I just simply sum up the total of the counts reported by HTSeq and divide it by the total number of unique reads? ...
written 1 day ago by morteza.aslanzadeh10
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How many of the reads end up being counted by HTSeq count
... I am new to these types of quality control checks. I have not faced any error in my analyses but want to perform quality control. I have aligned my sncRNA reads with bowtie (-m 1 option) and after making the bam output from the alignment I performed HTSeq count. Now I want to see if most of the read ...
assembly sequence rna-seq written 1 day ago by morteza.aslanzadeh10 • updated 1 day ago by Ido Tamir5.1k
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Answer: A: Don't let TopGo to trimm long GO names
... I found the answer in Github. So basically we have to add ```numChar=1000``` to ```all_res1``` i.e: ``` all_res1 <- GenTable(GOdata1, weightFisher=weight_fisher_result1, orderBy='weightFisher', topNodes=length(allGO1), numChar=1000) ``` numChar: truncates GO term descriptions at 1000 chars (bas ...
written 4 weeks ago by morteza.aslanzadeh10
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Don't let TopGo to trimm long GO names
... I'm using TopGo to do GO analyses. When I get my enriched terms, the long term names get corrupted. ```I have some text then ...```. For example: ``` GO:0000122 negative regulation of transcription by ... GO:0006886 intracellular protein transport GO:0010976 positive regulation of neuron projection ...
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Answer: A: Error with using getBM function in biomaRt
... It seems that there was a server error in ```ensembl```. I ran my code again and again (without any change) and finally, it completed the downloading without any error ...
written 5 weeks ago by morteza.aslanzadeh10
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Comment: C: Error with using getBM function in biomaRt
... I couldn't understand exactly what you just recommended. Since I need all the background genes for GO analyses how reliable it is to cut them in batches of 5000 genes? ...
written 5 weeks ago by morteza.aslanzadeh10
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Comment: C: Error with using getBM function in biomaRt
... When I tried to use this with fewer genes it worked. Isn't this because of the server error? I was also getting an unusual ensemble error when I was trying to download some data manually. ...
written 5 weeks ago by morteza.aslanzadeh10
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Comment: C: Error with using getBM function in biomaRt
... `bg_genes` class is character and the output for the second command is `character 22287` ...
written 5 weeks ago by morteza.aslanzadeh10 • updated 5 weeks ago by RamRS27k
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Error with using getBM function in biomaRt
... I have search a lot of online sources to solve this problem but couldn't. I'm using ```getBM()``` function of biomaRt but getting an error. I have used this code like 7 months ago without any error but now it's giving error and I think it should probably be because of the server ???? what I use: ` ...
software error R biomart rna-seq written 5 weeks ago by morteza.aslanzadeh10

Latest awards to morteza.aslanzadeh

Scholar 4 weeks ago, created an answer that has been accepted. For A: Error with using getBM function in biomaRt
Scholar 5 weeks ago, created an answer that has been accepted. For A: Error with using getBM function in biomaRt

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