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I am currently using STAR diploid version 2.7.11b to map RNA-seq reads to a diploid genome. I have referred to the STAR manual, but I still have two questions regarding the output:
When checking the chrName.txt file generated during genome indexing, I see chromosome names like chr1_h1, chr2_h1, ..., chr1_h2, chr2_h2,... and so on. Does h1 and h2 indicate haplotype 1 and haplotype 2, respectively?
While mapping, I specified ha in --outSAMattributes. Upon checking the ha attribute in the output BAM file, I found only ha:i:0 and ha:i:16908800. Did I make a mistake in any of the steps?
STAR --runThreadN 4 \
--genomeDir /home/ayumi/genome_index/HG00097 \
--readFilesIn /home/ayumi/RNAdata/HG00097/ERR188231_1.fastq.gz /home/ayumi/RNAdata/HG00097/ERR188231_2.fastq.gz \
--readFilesCommand zcat \
--outSAMtype BAM SortedByCoordinate \
--outSAMstrandField intronMotif \
--outSAMattributes NH HI AS nM NM MD jM jI MC ch ha \
--twopassMode Basic \
--outFileNamePrefix /home/ayumi/bams/HG00097/HG00097_diploid_
Initially, I set --outSAMattributes All ha, but no ha attributes were included. When I used only --outSAMattributes ha, the ha attribute in the output file showed only ha:i:0 and ha:i:16843008.
If there are any resources that could help solve this issue, please let me know.
Thank you!
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Hello,
I am currently using STAR diploid version 2.7.11b to map RNA-seq reads to a diploid genome. I have referred to the STAR manual, but I still have two questions regarding the output:
When checking the
chrName.txt
file generated during genome indexing, I see chromosome names likechr1_h1
,chr2_h1
, ...,chr1_h2
,chr2_h2
,... and so on. Doesh1
andh2
indicate haplotype 1 and haplotype 2, respectively?While mapping, I specified
ha
in--outSAMattributes
. Upon checking theha
attribute in the output BAM file, I found onlyha:i:0
andha:i:16908800
. Did I make a mistake in any of the steps?Here are the commands I used:
Generating genome indexes:
Running mapping jobs:
Initially, I set
--outSAMattributes All ha
, but no ha attributes were included. When I used only--outSAMattributes ha
, the ha attribute in the output file showed onlyha:i:0
andha:i:16843008
.If there are any resources that could help solve this issue, please let me know.
Thank you!
Best regards,
Ayumi
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