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DaehwanKimLab / hisat2

Graph-based alignment (Hierarchical Graph FM index)
GNU General Public License v3.0
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`hisat-3n-table` do not count the bases correctly. #292

Closed y9c closed 3 years ago

y9c commented 3 years ago

For pair-end reads mapping, the R1 and R2 of a identical fragment might overlap with a certain window. But hisat-3n-table do not deal with this correctly, and report duplicated results for this window, which will over estimate the coverage of the data.

imzhangyun commented 3 years ago

Thank you for identify the problem. Please pull the newest script for HISAT-3N and make again. We just solved the multiple counting problem in same read.

Best, Yun (Leo)

y9c commented 3 years ago

Thank you @imzhangyun .

I would like to known can hisat-3n-table take bam format as input instead of sam format?

imzhangyun commented 3 years ago

Unfortunately current hisat-3n-table does not support BAM file as input. We may add this option in future version.

Best, Leo

y9c commented 3 years ago

Thank you very much.

On Sat, Jun 5, 2021 at 8:54 PM Yun (Leo) Zhang @.***> wrote:

Unfortunately current hisat-3n-table does not support BAM file as input. We may add this option in future version.

Best, Leo

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imzhangyun commented 3 years ago

Good news! hisat-3n-table now accept standard input stream as alignment result. If you have sorted bam file, you can use hisat-3n-table as: samtools view -h sorted_alignment_result.bam | hisat-3n/hisat-3n-table --ref genome.fa --alignments - --output-name output.tsv --base-change C,T

Please notice that we also changed some input arguments' name. For more detail, please check the hisat-3n homepage.

Best, Leo

y9c commented 2 years ago

Hi @imzhangyun,

Is it possible to write the output into stdout? So I can compress the file within one pipe. raw tsv output take too much space.

Thank you!

imzhangyun commented 2 years ago

Hello @yech1990

Please check the branch "hisat-3n_ZF".

Now you have option to output into stdout. If you use the option --output-name <outputFile>, hisat-3n-table will output to the file. If you run hisat-3n-tablewithout --output-name <outputFile> option, hisat-3n-table will output to stdout. I tested it on my side and everything works fine. Could you also try it and give me some feedback? If it works well, I will merge the "hisat-3n_ZF" branch to "hisat-3n" branch.

Best, Leo