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Troubles while creating snap file with bam #253

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HieuNg1598 opened this issue Nov 19, 2022 · 0 comments
Open

Troubles while creating snap file with bam #253

HieuNg1598 opened this issue Nov 19, 2022 · 0 comments

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@HieuNg1598
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I am trying to create snap file using possorted.bam but I have got this problem during dealing with header sam file.
Do you know what is the problem ?
ERROR:
cat <( cat possorted.header.sam )\

<( samtools view possorted_bam.bam | awk '{for (i=12; i<=NF; ++i) { if ($i ~ "^CB:Z:"){ td[substr($i,1,2)] = substr($i,6,length($i)-5); } }; printf "%s:%s\n", td["CB"], $0 }' )
| samtools view -bS -> tbi_possorted.snap.bam
cat: /dev/fd/63/dev/fd/62: Not a directory
[main_samview] fail to read the header from "-".

Hope to hear from you soon

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