User: alireza346

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alireza3460
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Posts by alireza346

<prev • 19 results • page 1 of 2 • next >
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(Closed) single base resolution count at the genome level
... I am trying to get the single base resolution bedgraph file at the genome level . do you know how to do that? in fact, I have DNAseq data and trying to get the read count per base per gene. ...
sequencing written 28 days ago by alireza3460
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right genomic coordinate of each gene
... I have got the genomic coordinates from UCSC and here is a small example of the file. small example: chr10 + 126490353 126525239 FAM175B chr10 + 126628971 126676005 ZRANB1 chr10 + 126630691 126676005 ZRANB1 chr10 - 126676417 126694582 CTBP2 chr10 - 126676417 126716453 CTBP2 ...
gene next-gen written 4 weeks ago by alireza3460 • updated 4 weeks ago by lieven.sterck3.3k
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strand identification from sam file
... I have `.sam` files from RNAseq alignment. the alignment was done using `Tophat`. now, I am trying to split the forward and reverse strands and make two `sam` files for forward and reverse strands separately. in my `sam` file I found 4 numbers (codes) to identify strands. the numbers are `0, 16, 27 ...
alignment rna-seq written 5 weeks ago by alireza3460
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read strand identification from sam file
... I have `sam` files (aligned RNAseq to `genome`) and `converted the bam files to sam` file. I am working with python. in my pipeline I need to know the `strand of the reads`. the following lines are 2 examples of the reads that I have in my sam file: D00645:305:CCVLRANXX:1:1104:13111:49466 272 c ...
alignment rna-seq written 6 weeks ago by alireza3460 • updated 6 weeks ago by Pierre Lindenbaum115k
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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 8 weeks ago by alireza3460 • updated 8 weeks ago by jared.andrews071.7k
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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 weeks 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 11 weeks ago by alireza3460 • updated 11 weeks 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 3 months ago by alireza3460 • updated 3 months ago by btsui280
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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 4 months 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 5 months ago by alireza3460

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