Kilian Leon Kleemann
Kilian Leon Kleemann
Dear Ben, bowtie2 version: 2.4.2 Command: mkdir SAM_files cat sample_list.txt | while read sample; do bowtie2 -p 12 -q --local -x mm10 -1 fastq/trimmed_reads/${sample}.1.trimmed.fastq.gz -2 fastq/trimmed_reads/${sample}.2.trimmed.fastq.gz -S SAM_files/${sample}.unsorted.sam done Everything...
@gireeshkbogu @genecell Same!
I have tried now to install the tbb file with brew because i seem to get an error with recognizing the _dyld: Library not loaded: @rpath/libtbb.dylib_ Do you have any...
I made sure the reformatting of GTF is correct: ``` wget https://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/rmsk.txt.gz gzip -d *.gz talon_reformat_gtf -g reference/GRCh38_GENCODE_rmsk_TE.gtf talon_initialize_database --f reference/GRCh38_GENCODE_rmsk_TE_reformatted.gtf \ --g hg38_rmsk_ucsd \ --a hg38 \ --o hg38...
Should be able to download the gtf and unzp with the first command - thats the one I tried
Which gtf did you use for hg38 repeatmasker?
Hi Ying, thank you for your response. I am a bit confused still since I downloaded all fastq data and for example in the direct RNAseq for the H9 cells...
aws s3 sync --no-sign-request s3://sg-nex-data/data/sequencing_data_ont/fastq/ . did this for downloadling all data - and obvs. replace with specific folder name for specific download
thx this helped!