Feltyq wrote:These are 3 samples with RNA sequencing data. You will need to combine all the fastq files for each sample before alignment.
cwyoo wrote:Feltyq wrote:These are 3 samples with RNA sequencing data. You will need to combine all the fastq files for each sample before alignment.
Here are the tools that have been used to analyze the next-generation sequencing reads (RNA or DNA):
HISAT2 (see https://ccb.jhu.edu/software/hisat2/index.shtml)
htseq-count (module from HTSeq 0.6.1p1 see http://www-huber.embl.de/HTSeq/doc/count.html)
Gene Name (GTF file) downloaded from ftp://ftp.ensembl.org/pub/release-84/gtf/homo_sapiens/Homo_sapiens.GRCh38.84.chr_patch_hapl_scaff.gtf.gz
cwyoo wrote:cwyoo wrote:Feltyq wrote:These are 3 samples with RNA sequencing data. You will need to combine all the fastq files for each sample before alignment.
Here are the tools that have been used to analyze the next-generation sequencing reads (RNA or DNA):
HISAT2 (see https://ccb.jhu.edu/software/hisat2/index.shtml)
htseq-count (module from HTSeq 0.6.1p1 see http://www-huber.embl.de/HTSeq/doc/count.html)
Gene Name (GTF file) downloaded from ftp://ftp.ensembl.org/pub/release-84/gtf/homo_sapiens/Homo_sapiens.GRCh38.84.chr_patch_hapl_scaff.gtf.gz
Attached are the sorted counts.
cwyoo wrote:
Here are the tools that have been used to analyze the next-generation sequencing reads (RNA or DNA):
HISAT2 (see https://ccb.jhu.edu/software/hisat2/index.shtml)
htseq-count (module from HTSeq 0.6.1p1 see http://www-huber.embl.de/HTSeq/doc/count.html)
Gene Name (GTF file) downloaded from ftp://ftp.ensembl.org/pub/release-84/gtf/homo_sapiens/Homo_sapiens.GRCh38.84.chr_patch_hapl_scaff.gtf.gz
cwyoo wrote:cwyoo wrote:
Here are the tools that have been used to analyze the next-generation sequencing reads (RNA or DNA):
HISAT2 (see https://ccb.jhu.edu/software/hisat2/index.shtml)
htseq-count (module from HTSeq 0.6.1p1 see http://www-huber.embl.de/HTSeq/doc/count.html)
Gene Name (GTF file) downloaded from ftp://ftp.ensembl.org/pub/release-84/gtf/homo_sapiens/Homo_sapiens.GRCh38.84.chr_patch_hapl_scaff.gtf.gz
For the new analysis, following versions have been used:
HISAT2 2.0.5 (release 11/4/2016)
htseq-count HTSeq 0.6.1p1
Gene Name (GTF file) downloaded from ftp://ftp.ensembl.org/pub/release-87/gtf/homo_sapiens/Homo_sapiens.GRCh38.87.chr_patch_hapl_scaff.gtf.gz
cwyoo wrote:cwyoo wrote:cwyoo wrote:
Here are the tools that have been used to analyze the next-generation sequencing reads (RNA or DNA):
HISAT2 (see https://ccb.jhu.edu/software/hisat2/index.shtml)
htseq-count (module from HTSeq 0.6.1p1 see http://www-huber.embl.de/HTSeq/doc/count.html)
Gene Name (GTF file) downloaded from ftp://ftp.ensembl.org/pub/release-84/gtf/homo_sapiens/Homo_sapiens.GRCh38.84.chr_patch_hapl_scaff.gtf.gz
For the new analysis, following versions have been used:
HISAT2 2.0.5 (release 11/4/2016)
htseq-count HTSeq 0.6.1p1
Gene Name (GTF file) downloaded from ftp://ftp.ensembl.org/pub/release-87/gtf/homo_sapiens/Homo_sapiens.GRCh38.87.chr_patch_hapl_scaff.gtf.gz
Using the above settings, these are ID3chipseq analyses results.
./srapath SRR######
./fastq-dump SRR######
./hisat2-build `ls *fasta | awk '{printf("%s,"$1)}' | sed -e 's/,$//'` HT2_IDX
./hisat2 -x ./grch38/genome -U SRR######.fastq -S alignedfile.sam
python -m HTSeq.scripts.count -m intersection-nonempty -s no -i gene_name ~/Desktop/HISAT2/alignedfile.sam ~/Desktop/genome.gtf -o Outputfile.samout > Outputfile_Counts.txt
./bowtie2 -x ./Bowtie2Index/genome -U ~/Sample-A-Input_S43_L007_R1_001.fastq -S BowTie_Sample_A_Input2.sam
grep GENE_NAME htseq_count_output.sam > gene_info.txt
grep APOE COUNTDrRoy_Bowtie.sam > DrRoy_APOE_Bowtie.txt
sort -t$'\t' -k4,4g gene_info.txt > sorted_gene_info.txt
sort -t$'\t' -k4,4g DrRoy_APOE_Bowtie.txt > sort_DrRoy_APOE_Bowtie.txt
Users browsing this forum: No registered users and 3 guests