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jmbreda / Sanity

Filtering of Poison noise on a single-cell RNA-seq UMI count matrix
GNU General Public License v3.0
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not enough fields on line number 0 #6

Closed qiaochen closed 3 years ago

qiaochen commented 3 years ago

Hello, thank you for releasing your work. I was trying to test your wonderful tool on 3k PBMC dataset. It was a .mtx matrix, and running Sanity encountered an error showing "not enough fields on line number 0". Is Sanity trying to read the headlines?

jmbreda commented 3 years ago

Hi qiaochen, thank you for your interest in Sanity. Sanity ignores the first commented lines (starting with %), then it expects in the first non-commented line; total number of gene IDs, total number of cells IDs, total number of lines (see https://math.nist.gov/MatrixMarket/formats.html for more details on .mtx format). However, this error seems to indicate that Sanity did not recognize the input as a .mtx file. Is your input file extension .mtx? Is is it decompressed?

qiaochen commented 3 years ago

Many thanks, Breda! Indeed, the problem lies in the .mtx file, which was not completely transferred due to an unsuccessful scp command.