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I am aligning my Small RNA Seq data with Bowtie 2. Although the alignment performs well, the only information I obtain after finishing running the alignment is the following:

## Time loading reference: 00:00:00
## Time loading forward index: 00:00:00
## Time loading mirror index: 00:00:00
## Multiseed full-index search: 00:00:00
## Time searching: 00:00:00
## Overall time: 00:00:00
## Time loading reference: 00:00:00
## Time loading forward index: 00:00:00
## Time loading mirror index: 00:00:00
## Multiseed full-index search: 00:00:01
## Time searching: 00:00:01
## Overall time: 00:00:01
## Time loading reference: 00:00:00
## Time loading forward index: 00:00:00
## Time loading mirror index: 00:00:00
## Multiseed full-index search: 00:00:00
## Time searching: 00:00:00
## Overall time: 00:00:00
## Time loading reference: 00:00:00
## Time loading forward index: 00:00:00
## Time loading mirror index: 00:00:00
## Multiseed full-index search: 00:00:00
## Time searching: 00:00:00
## Overall time: 00:00:00
## Time loading reference: 00:00:00
## Time loading forward index: 00:00:00
## Time loading mirror index: 00:00:00
## Multiseed full-index search: 00:00:00
## Time searching: 00:00:00
## Overall time: 00:00:00
## Time loading reference: 00:00:00
## Time loading forward index: 00:00:00
## Time loading mirror index: 00:00:00
## Multiseed full-index search: 00:00:00
## Time searching: 00:00:00
## Overall time: 00:00:00

This is my command line to build the index: bowtie2-build -o 3 -t 5 Nuevofastaorina human_mirs

And this is my command line to do the alignment:

bowtie2 -x human_mirs -U 1.lane.clean.gz -N 1 --norc --no-unal --no-head --ignore-quals –-quiet > sr1prueba.sam

Does anyone know how to obtain an alignment summary instead of the above information? What I mean by alignment summary is the following:

20000 reads; of these:
  20000 (100.00%) were unpaired; of these:
    1247 (6.24%) aligned 0 times
    18739 (93.69%) aligned exactly 1 time
    14 (0.07%) aligned >1 times
93.77% overall alignment rate
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  • $\begingroup$ Please show the first few lines of your fastq input data (i.e. lane.clean.gz). This should help to diagnose the problem. $\endgroup$
    – gringer
    Oct 19, 2023 at 3:21

2 Answers 2

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Remove the --quiet option, and capture STDERR as well as STDOUT:

bowtie2 -x human_mirs -U 1.lane.clean.gz -N 1 --norc --no-unal --no-head --ignore-quals 1>sr1prueba.sam 2>sr1prueba.summary.log

See also:

bowtie2 manual: alignment summary

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Get samtools.

Then run:

samtools stats file.bam

and/or

samtools flagstat file.bam

For example outputs see here.

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