alignReadsChunk: Genomic alignment
In HTSeqGenie: A NGS analysis pipeline.
Description
Usage
Arguments
Details
Value
Description
Genomic alignment using gsnap.
Usage
1
alignReadsChunk(fp1, fp2 = NULL, save_dir = NULL)
Arguments
fp1
Path to FastQ file
fp2
Path to second FastQ file if paired end data, NULL if single ended
save_dir
Save directory
Details
Aligns reads in fp1 and fp2 to genome specified via
global config variable alignReads.genome. Gsnap output
is converted into BAM files and sorted + indexed.
Value
List of alignment files in BAM format
HTSeqGenie documentation built on Nov. 8, 2020, 6:12 p.m.
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Description Usage Arguments Details Value
Description
Genomic alignment using gsnap.
Usage
1 | alignReadsChunk(fp1, fp2 = NULL, save_dir = NULL)
|
Arguments
fp1 |
Path to FastQ file |
fp2 |
Path to second FastQ file if paired end data, NULL if single ended |
save_dir |
Save directory |
Details
Aligns reads in fp1 and fp2 to genome specified via global config variable alignReads.genome. Gsnap output is converted into BAM files and sorted + indexed.
Value
List of alignment files in BAM format
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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