I have 4 lane , single end reads fastq files per sample that I need to align. How can I combine the 4 lanes to give as input?
I am trying to give the following command:
hisat2 -p 12 -x ./MM10_Index_HISAT/mm10 -U ./Rane_data/Acrolein-1_S4_L1_R1.fastq,./Rane_data/Acrolein-1_S4_L2_R1.fastq,./Rane_data/Acrolein-1_S4_L3_R1.fastq,./Rane_data/Acrolein-1_S4_L4_R1.fastq --rna-strandedness F -S ./HISAT_output
Also, how can I give all samples together in one command? I have 6 samples.
2 answers
Yes, that is correct, see manual.
-U <r>
Comma-separated list of files containing unpaired reads to be aligned, e.g. lane1.fq,lane2.fq,lane3.fq,lane4.fq. Reads may be a mix of different lengths. If - is specified, hisat2 gets the reads from the “standard in” or “stdin” filehandle.
Error: Encountered internal HISAT2 exception (#1)
Command: /usr/local/hisat2/hisat2-2.1.0/hisat2-align-s --wrapper basic-0 -p 12 -x ./MM10_Index_HISAT/mm10 --rna-strandedness F -S ./HISAT_output -U ./Rane_data/Acrolein-1_S4_L1_R1.fastq,./Rane_data/Acrolein-1_S4_L2_ R1.fastq,./Rane_data/Acrolein-1_S4_L3_R1.fastq,./Rane_data/Acrolein-1_S4_L4_R1.fastq,./Rane_data/Acrolein-2_S5_L1_R1.fastq,./Rane_data/Acrolein-2_S5_L2_R1.fastq,./Rane_data/Acrolein-2_S5_L3_R1.fastq,./Rane_data/Acro lein-2_S5_L4_R1.fastq,./Rane_data/Acrolein-3_S6_L1_R1.fastq,./Rane_data/Acrolein-3_S6_L2_R1.fastq,.//Rane_data/Acrolein-3_S6_L3_R1.fastq,./Rane_data/Acrolein-3_S6_L4_R1.fastq,./Rane_data/Control-1_S1_L1_R1.fastq,./R ane_data/Control-1_S1_L2_R1.fastq,./Rane_data/Control-1_S1_L3_R1.fastq,./Rane_data/Control-1_S1_L4_R1.fastq,./Rane_data/Control-2_S2_L1_R1.fastq,./Rane_data/Control-2_S2_L2_R1.fastq,./Rane_data/Control-2_S2_L3_R1.fa stq,./Rane_data/Control-2_S2_L4_R1.fastq,./Rane_data/Control-3_S3_L1_R1.fastq,./Rane_data/Control-3_S3_L2_R1.fastq,./Rane_data/Control-3_S3_L3_R1.fastq,./Rane_data/Control-3_S3_L4_R1.fastq (ERR): hisat2-align exited with value 1
hisat2 -p 12 -x ./MM10_Index_HISAT/mm10 -U ./Rane_data/Acrolein-1_S4_L1_R1.fastq,./Rane_data/Acrolein-1_S4_L2_R1.fastq,./Rane_data/Acrolein-1_S4_L3_R1.fastq,./Rane_data/Acrolein-1_S4_L4_R1.fastq --rna-strandedness F -S ./HISAT_output
Right now this is my command line I am giving and it is also giving me error:
Error:
Encountered internal HISAT2 exception (#1)
Command:
/usr/local/hisat2/hisat2-2.1.0/hisat2-align-s --wrapper basic-0 -p 12 -x ./MM10_Index_HISAT/mm10 --rna-strandedness F -S ./HISAT_output -U ./Rane_data/Acrolein-1_S4_L1_R1.fastq,./Rane_data/Acrolein-1_S4_L2_
R1.fastq,./Rane_data/Acrolein-1_S4_L3_R1.fastq,./Rane_data/Acrolein-1_S4_L4_R1.fastq
(ERR): hisat2-align exited with value 1
Also I downloaded the tar file of the mm10. The following are the files and contents in the mm10 folder.
total 3961472
-rw------- 1 a0malh01 unixuser 888467914 Mar 17 2016 genome.1.ht2
-rw------- 1 a0malh01 unixuser 663195880 Mar 17 2016 genome.2.ht2
-rw------- 1 a0malh01 unixuser 6119 Mar 17 2016 genome.3.ht2
-rw------- 1 a0malh01 unixuser 663195875 Mar 17 2016 genome.4.ht2
-rw------- 1 a0malh01 unixuser 1165549977 Mar 17 2016 genome.5.ht2
-rw------- 1 a0malh01 unixuser 675339278 Mar 17 2016 genome.6.ht2
-rw------- 1 a0malh01 unixuser 8 Mar 17 2016 genome.7.ht2
-rw------- 1 a0malh01 unixuser 8 Mar 17 2016 genome.8.ht2
-rwx------ 1 a0malh01 unixuser 1378 Mar 17 2016 make_grcm38.sh
Just wanted to make sure it is fine and not causing any error.
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