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DaehwanKimLab / hisat-genotype

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No typing and assembly results output #53

Open wshuai294 opened 3 years ago

wshuai294 commented 3 years ago

Hi Chris,

I found that there is no output for some samples. I have uploaded one typical fastq file on https://drive.google.com/drive/folders/1AweXKKjIO1UzRHc7A68UMi2PRo4JBJxU?usp=sharing

Could you please help me to test if you can get the output with this sample?

Thanks, WANG Shuai

chbe-helix commented 3 years ago

Hi Wang,

It may take me awhile to get to testing it myself. I might suggest trying to see if you can align those files to the genotype_genome using HISAT2. Alternatively, you can run HISAT-genotype and keep the BAM file and extracted reads to see if everything is aligned and properly parsed.

--keep-alignment for keeping the BAM files --keep-extract for keeping extracted reads

Thanks, Chris

wshuai294 commented 3 years ago

Hi Chris,

We have added the parameters, the BAM and reads file seems normal. However, the report file contains nothing. Could you please help me to check them kindly? I have uploaded these files to https://drive.google.com/drive/folders/1AweXKKjIO1UzRHc7A68UMi2PRo4JBJxU?usp=sharing.

Thanks, WANG Shuai

chbe-helix commented 3 years ago

Hi WANG Shuai,

It doesn't look like I can download or view any of the files loaded to the Drive.

Thanks, Chris

wshuai294 commented 3 years ago

Hi Chris,

I have sent the file to your email address, please kindly check.

Best, WANG Shuai

chbe-helix commented 3 years ago

Hi WANG Shuai,

I am not able to reproduce the issue you are having. You may want to try running the following command and check the report file output for the results.

hisatgenotype --keep-extract  --base hla --locus-list A,B,C,DPA1,DPB1,DQA1,DQB1,DRB1 -1 HLA_24_T_50-50.read1.fastq.gz -2 HLA_24_T_50-50.read2.fastq.gz

Thanks, Chris

wshuai294 commented 3 years ago

Hi Chris,

I found I got no assembly output in the case of the same bug mentioned in #38, and I am waiting for you to figure it out.

Thanks. WANG Shuai

asangphukieo commented 2 years ago

Dear WANG Shuai,

I also found this issue with my samples. Is there any update for solving this issue?

Thank you,

wshuai294 commented 2 years ago

Dear WANG Shuai,

I also found this issue with my samples. Is there any update for solving this issue?

Thank you,

Hello,

I have no idea about the update, you can observe the comments in https://github.com/DaehwanKimLab/hisat-genotype/issues/38 for related information.

Best,