Does Last aligner only outputs the mapped reads to a bam file ?
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3.2 years ago
pinn ▴ 130

Hi, I used Last on Illumina genome dataset, after generating bam file its showing only mapped reads. I'm not able to figure it out. Why it is not showing any other statistics ?

Aligner - Last
Data-set - Human genome
Read-length - Illumina 250 bp (PE reads)

##CMD##
./lastal -Q1 -P10 hg38 lastl/SRR1q26.fastq lastl/SRR2q26.fastq > SRR.maf
After converting SRR.maf ----> SRR.last.bam

##CMD##
`samtools flagstat SRR.last.bam`
1067609571 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
**1067609571 + 0 mapped (100.00% : N/A)**
0 + 0 paired in sequencing
0 + 0 read1
0 + 0 read2
0 + 0 properly paired (N/A : N/A)
0 + 0 with itself and mate mapped
0 + 0 singletons (N/A : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)

Is it problem with the alignment ? How to sort it out. Thanks!

assembly alignment sequencing next-gen genome • 1.2k views
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I'm curious - is this a valid use for lastal? The website says it does local alignments from FASTA files to genomes, why are you using this on FASTQ reads that come with a lot of possibilities for sequencing error and whatnot?

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To put it differently, why not use one of the tried and extensively tested programs, such as bwa, bowtie2, hisat2, star, bbmap?

edit: never mind my comment, you indeed have been testing several different programs:

Comparing alignment stats BWAmem vs. Soap2 aligner

gSNAP aligner generating truncated sam file ?

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Definitely not. Last is an aligner like Blast and Clustal are aligners. It's not a mapper.

LAST ~= (BLAST - B)

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Which is why I asked OP. Technically, local alignment for reads makes a little sense, as reads are sequences after all. But one should be aligning reads semi-globally, so they are aligned globally, but the alignment is local to the database sequence. I don't understand OP's logic behind using local alignments on reads.

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I have the same problem on that, some papers do have used the last to mapping the Metatranscriptomic data to the protein database, but I wonder how to filter the result by the output file.

paper link: https://www.pnas.org/content/112/17/5443

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