i used bowtie2 without problems on many files which worked great, now it gives the error message: "Read xyz has more quality values than read characters" I re - downloaded the fastq file, same problem.
gives the following:
@SRR1191170.1 1/1 T012122020210210110200211200001113113312113321..331 + !JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ338&5554 @SRR1191170.2 2/1 T01212202021021011020021120000111311331211332133331 + !JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ32913444 @SRR1191170.3 3/1 T30122212022122110022001201102011112320012302211120
The url of the file was: ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR119/000/SRR1191170/SRR1191170_2.fastq.gz
What can i do to make this file more digestible for bowtie2?
I tried to install fqtools with bioconda to see if there is an option to remedy this, but starting the fqtools also left me with an error message.
I currently do not know how to compile / install it manually on mac.
dyld: Library not loaded: @rpath/libdeflate.so Referenced from: /Users/normanreppingen/anaconda3/lib/libhts.1.9.dylib Reason: image not found Abort trap: 6
I need to know what these cancer associated fibroblasts are doing, but i am facing challenges...
Is there a helpful parameter for bowtie2 which i do not know?
P.S.: I bought the Biostar Handbook recently, and read carefully about bowtie2 - but this error really seems to be an exception.