User: alireza346

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alireza3460
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Posts by alireza346

<prev • 15 results • page 1 of 2 • next >
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cell type specific TAD coordinates and orientations for Hi-C
... do you guys know how I can predict `TAD` coordinates and orientations for `Hi-C` and `4C` data analysis for specific cells type. or if there is any `BED` file available containing `TAD` coordinates and orientations for specific cells, would you please let me know where I can find it? ...
sequencing written 1 day ago by alireza3460 • updated 1 day ago by jared.andrews071.3k
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isolate the output of lignment in fastq format
... I have `RNAseq` data and trying to align the `fastq` files to human `transcriptome` (not `genome`). I want to isolate the reads that map to mRNA transcriptome in `fastq` format. I am using `bowtie2`. do you know how I can get the output of `bowtie2` as `fastq` file? ...
rna-seq written 9 days ago by alireza3460
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filtering the reads based on the length
... I have a fastq file (RNAseq) and filtered the linkers. now the sequences in the file have different length. I want to remove the reads with shorter than 21 nucleotide and use the rest of the reads. do you know any toll to do that? ...
rna-seq written 24 days ago by alireza3460 • updated 24 days ago by karthic90
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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 9 weeks ago by alireza3460 • updated 9 weeks ago by btsui270
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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 9 weeks 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 3 months 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 3 months ago by alireza3460 • updated 3 months ago by finswimmer6.2k
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Comment: C: blat the RNAseq data of organoids generated from mouse
... yes the adapters are trimmed ...
written 4 months 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 4 months ago by alireza3460
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Comment: C: extracting the longest transcript in a fasta file
... it dies not return any output ...
written 4 months ago by alireza3460

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