User: alireza346

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alireza3460
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Posts by alireza346

<prev • 12 results • page 1 of 2 • next >
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make a new bam file
... I have a set of genes including 105 genes. I want to make a new bam file excluding these 105 genes. do you know how I can do that? ...
rna-seq written 6 days ago by alireza3460 • updated 6 days ago by btsui230
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frame frequency analysis per position per gene
... I have ribosome profiling data and I have aligned the files. I want to get the frame frequency for each codon (basically for each position of the codon) per gene. do you know how I can do that? ...
sequencing written 11 days ago by alireza3460
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coverage of the reads over coding sequence only for one gene
... I have `RNAseq` data and trying to get the coverage of the reads over coding sequence but only for one gene for example `GAPDH`. and plot the coverage in this way: in fact the `y-axis` would be coverage or normalized read count and `x-axis` would be the coding sequence. but the coding sequence which ...
rna-seq written 6 weeks ago by alireza3460
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making the gene specific bam file
... I have RNAseq data and aligned the fastq files to the genome. so now I have bam file. I want to make the bam file only for one gene for example gapdh. to do so at first I have converted the bam file to sam file to be able to grep it. in the sam file we only have coordinates but when I tried to look ...
rna-seq written 7 weeks ago by alireza3460 • updated 7 weeks ago by finswimmer4.5k
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Comment: C: blat the RNAseq data of organoids generated from mouse
... yes the adapters are trimmed ...
written 9 weeks ago by alireza3460
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blat the RNAseq data of organoids generated from mouse
... I have `RNAseq` data from `organoids` were generated from `mouse`. I tried to `blat` many of the reads on `UCSC` (against `mm10` genome) but I got this error: "`Sorry, no matches found`". the reads were selected from different parts of the `fastq files`. do you know what the problem could be? ...
rna-seq written 9 weeks ago by alireza3460
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Comment: C: extracting the longest transcript in a fasta file
... it dies not return any output ...
written 10 weeks ago by alireza3460
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Comment: C: extracting the longest transcript in a fasta file
... actually these are not working for my question ...
written 10 weeks ago by alireza3460
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5 follow
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extracting the longest transcript in a fasta file
... I have a fasta file like this example: >ENST00000511961.1|ENSG00000013561.13|OTTHUMG00000129660.5|OTTHUMT00000370661.3|RNF14-003|RNF14|278 MSSEDREAQEDELLALASIYDGDEFRKAESVQGGETRIYLDLPQNFKIFVSGNSNECLQNSGFEYTICFLPPLVLNFELPPDYPSSSPPSFTLSGKWLSPTQLSALCKHLDNLWEEHRGSVVLFAWMQFLKEETLAYLNIVSPFELK ...
gene written 10 weeks ago by alireza3460 • updated 10 weeks ago by WouterDeCoster31k
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mitochondrial tRNA database
... I am looking for a database to get the sequences of mitochondrial tRNAs. do you know where I can find them? ...
next-gen written 3 months ago by alireza3460 • updated 3 months ago by genomax54k

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