User: akhan

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akhan0
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Posts by akhan

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Comment: C: Annotae with Transcript IDs for the chromosome coordinates in SJ.ou.tab files ge
... Hi, Thanks for your reply. I have tried with bedtools, bedops and the gtf file to get transcript ID for the chromosome coordinate in sj.out.tab file, but it generates completely different coordinates for the bed files and using bedop tools I also tried to map bed file to gtf with no luck having s ...
written 9 days ago by akhan0
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Annotae with Transcript IDs for the chromosome coordinates in SJ.ou.tab files generated bu STAR aligner
... Hi, I aligned some of my RNA_seq samples Using STAR aligner. The command I used to align the samples shown below: #to create count files and splice junction files. STAR --genomeDir ./mouse_genome_test --runThreadN 12 --runMode alignReads --outSAMtype BAM SortedByCoordinate Unsorted \ ...
genome assembly alignment rna-seq sequencing written 9 days ago by akhan0 • updated 9 days ago by genomax71k
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ERROR In aligmnet of RNA_seq data using STAR aligner_updated
... Hi, I am new to a lot of the bioinformatic tools that are available to do the alignment of RNA-seq data. Currently, I am using STAR aligner to do some alignment on my data. I have successfully created a genome index and aligned my data using the following commands STAR --runMode --runThreadN ...
genome alignment rna-seq written 11 days ago by akhan0 • updated 11 days ago by genomax71k
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(Closed) ERROR In aligmnet of RNA_seq data using STAR aligner
... Hi, I am new to a lot of the bioinformatic tools that are available to do the alignment of RNA-seq data. Currently, I am using STAR aligner to do some alignment on my data. I have successfully created a genome index and aligned my data using the following commands STAR --runMode --runThreadN 30 g ...
alignment rna-seq written 11 days ago by akhan0
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How to get output of phenotype index according to p values obtained from FAST-LMM association study
... Hi, I am using FAST LMM to do an association study with the following command. ./FaSTLMM.207c/Bin/Linux_MKL/fastlmmc -verboseOutput -bfile xaj_pp -bfilesim xaj_pp -pheno pheno_w_header.txt -covar human_profile_Covariates_fast_LMM.txt -mpheno 50201 -out FAST_LMM_result_10.txt. I have SNP dataset ...
genome software error snp rna-seq written 2.4 years ago by akhan0
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Bwa alignment problem of single end DNA reads
... Hi, I am trying to align Genomic DNA sequence reads (64 bases in length) to reference human genome. The sequence reads are single ended. I am using bwa to align. My question is whether is it possible to align sequence reads by giving  a parameter option to zero mismatch. I want to extract reads tho ...
alignment bwa written 4.0 years ago by akhan0 • updated 4.0 years ago by dariober10k

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Popular Question 2.4 years ago, created a question with more than 1,000 views. For Bwa alignment problem of single end DNA reads

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