rnnh / bioinfo-notebook Goto Github PK

Hello,

Please change the following hard-coded line in UniProt_downloader.sh.

xargs -n 1 -P $PROCESSORS -I % curl -s https://www.uniprot.org/uniprot/%.fasta \

TO

xargs -n 1 -P $PROCESSORS -I % curl -s https://rest.uniprot.org/uniprotkb/%.fasta \

Without this curl cannot download files

Thanks
Abhijit

When the following command is run for human genome, I get the following error.
I tried writing a script to check if the fastq files had more 1024 chars but it did not. Can you please direct me to what i may be doing wrong.
thank you,
Deepta.

/Users/SBRGMBA/Downloads/MACE-1.2/bowtie-1.3.1-macos-x86_64/bowtie-align-s --wrapper basic-0 -S -q -m 1 -x /Users/SBRGMBA/Downloads/hg19_c.ebwt/hg19_c /Users/SBRGMBA/Downloads/MACE-1.2/rawSeqMACEexample/SRR346401.fastq CTCF_replicate1.sam
Reads file contained a pattern with more than 1024 quality values.
Please truncate reads and quality values and and re-run Bowtie

I followed the instructions from here
https://sourceforge.net/projects/chipexo/files/
https://github.com/rnnh/bioinfo-notebook
https://rnnh.github.io/bioinfo-notebook/docs/bowtie.html