How to get the alignment summary of HISAT2

Question

[Wet&DryImmunology]

Hi, I was trying to HISAT2, which is suppose to be the improved version of tophat or tophat2, HISAT publication , I applied it to my data, it was much much faster comparing with tophat2. I just a tinny issue, how could I get the "alignment summary" (information such as successful alignment rate)

I read the manual: "When HISAT2 finishes running, it prints messages summarizing what happened. These messages are printed to the "standard error" ("stderr") filehandle", how could I get my information from the filehandle?

I ran my command like:

nohup hisat2  -x ~/Tool/hisat2-2.0.3-beta/hisat2index/genome/genome -U sample.fastq -S sample.sam > nohup.out&

I checked the nohup.out file, there was nothing in it. I guess this is a dumb question. Thanks for any suggestion.

[WouterDeCoster]

If you run it in the standard way (without nohup and '&') it will nicely print the summary, which you can redirect to a file if you like, with at the end of your command the following:

2> summarymetrics.txt

But I would argue that the program is fast enough to run without nohup :p

[Wet&DryImmunology]

@WouterDeCoster ,Thanks. I think you are right. HISAT2 is fast enough, which makes nohup not necessary anymore. I got the habit of using nohup and & from experience with tophat(2)...

[amitunited0532]

Can I find alignment summary after completing job, I mean from SAM file ?

[Guillermosanz92]

yes, with samtools stats

Answer 1

[EVR]

HI, Try running HiSAT2 like following

hisat2 -x ~/Tool/hisat2-2.0.3-beta/hisat2index/genome/genome -U > sample.fastq -S sample.sam 2>summary.txt.

[Wet&DryImmunology]

@Tom. Thanks, basically let a txt file take filehandle.

Answer 2

[Arindam Ghosh]

You can also add --summary-file *.txt to ur command.

hisat2 -p INT --dta -x path_to_ref_genome_index -U/-1/-2 *.fastq.gz -S *.sam -un-gz filename --summary-file *.txt --met-file *.txt

Refer: https://ccb.jhu.edu/software/hisat2/manual.shtml