TopHat and Fastq with different Lane numbers
I have a very naive question will TopHat handle successfully in default conditions FastQ files merged from different lanes. I get a generic error TopHat failed. What will be best approach align Fastq fro different lanes separately then merge Bam?
Any suggestion pleas
• 1,825 views
•
link
updated
by
WouterDeCoster
•
written
by
kanwarjag
•
written
by
kanwarjag
1 answer
A suggestion to narrow down the origin of your error would be to use Tophat on just one of the fastq files and see if the error reproduces or not.
• 0 views
•
link
written
by
WouterDeCoster
Log in to answer this question.
More posts like this
-
How to handle paired and unpaired reads in RNAseq pipeline
written by mohamadelian1996 •
-
RNA-Seq multiple lane
written by MaxMin •
-
Concatenating fastq for the same sample or doing it separately and merge at the BAM stage ?
written by mohsamir2016 •
-
Samtools merge/ "The File BAM exists" warning
written by Qboy •
-
Merging the libraries
written by User000
-
Merging BAM vs concatenate FASTQ
written by nhaus •
-
input for Connor: FASTQ files from several lanes
written by lien
-
Merge fastq files from different lanes
written by shmaisrael •
-
Mapping with tophat2 and setting a Tophat2 output directory?
written by mirza
-
Mac operating system for bioinformatics
written by kanwarjag
