User: alirezamomeni707

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Posts by alirezamomeni707

<prev • 23 results • page 1 of 3 • next >
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Comment: C: counting ERCCs spike-ins in RNAseq data
... thanks. actually I have aligned to ERCC (made index from fasta file). but I do not have GTF file for that. actually this is the main problem ...
written 10 weeks ago by alirezamomeni7070
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counting ERCCs spike-ins in RNAseq data
... I have used ERCC spike-in in my RNAseq data. I have aligned my data and now I have bam files. to count the reads per gene I used htseq-count(which needs gtf file). I also have to count ERCC (I have 98 spike-in). I have fasta file of ERCCs. do you know how I can count the ERCCs? ...
rna-seq written 10 weeks ago by alirezamomeni7070 • updated 10 weeks ago by Charles Plessy2.2k
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removing adapters based on IDs not sequence
... I am using cutadapt to remove the adapters from fastq file. in the paper I got the data from it mentioned that they use P5 and P7 adapters. is there any option in cutadapt to remove this adapters without giving the sequence itself? ...
rna-seq written 11 weeks ago by alirezamomeni7070
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Comment: C: wrong bam file format
... no because I had a look at the reference file I used and chr numbers are there. ...
written 11 weeks ago by alirezamomeni7070
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wrong bam file format
... I am trying to align my `.fastq` file using `tophat` on transcriptom. the resulting `.bam` file look like this: @SQ SN:89720 LN:1312 @SQ SN:89721 LN:735 @SQ SN:89722 LN:5191 @SQ SN:89723 LN:361 @SQ SN:89724 LN:9056 @SQ SN:89725 LN:83 @SQ SN:89726 LN:2603 @SQ SN:89727 ...
rna-seq written 11 weeks ago by alirezamomeni7070 • updated 11 weeks ago by Devon Ryan71k
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counting the reads mapped only to the coding sequence
... I have aligned the RNAseq data to the transcriptome and have .bam files. now I want to count the reads that map to the coding sequence not the whole transcriptome. I usually use HTseq count to do so. do you guys know how to do that? ...
rna-seq written 3 months ago by alirezamomeni7070 • updated 3 months ago by h.mon9.0k
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uploading wig file on the UCSC
... I have `RNAseq` data and have made wig file to upload on `UCSC`. as you know the file size must be at most `500 MB`. I can not upload to the `UCSC`. do you have any solution? BTW, I made the `.wig` files using `HTSeq` in python. ...
rna-seq written 3 months ago by alirezamomeni7070 • updated 3 months ago by genomax34k
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problem with tRNAseq alignment
... I am trying to align tRNAseq data to the tRNA transcriptom. I made the index files using bowtie and trying to align using tophat. when I run the program for a single file I got this error: Warning: Empty fasta file: 'tophat_out/tmp/segment_juncs.fa' Warning: All fasta inputs were empty Error: E ...
rna-seq written 3 months ago by alirezamomeni7070
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Comment: C: alignment to a special part
... yes I have bam file. I can also download GTF FILE. ...
written 3 months ago by alirezamomeni7070
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alignment to a special part
... I have a RNA-seq data and want to get the proportion of reads that map to a window of `100pb` between `5'UTR` and `CDS` (`50 bp` at `5'UTR` and `50 bp` at the CDS). since I am using `Tophat` to align and `bowtie` to build indexes, I guess I have to get the sequence of that part to build indexes. do ...
rna-seq written 3 months ago by alirezamomeni7070 • updated 3 months ago by Istvan Albert ♦♦ 74k

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