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| = Usage = | | = Usage = |
| ./bam trimBam [inFile] [outFile] [num-bases-to-trim-on-each-side] | | ./bam trimBam [inFile] [outFile] [num-bases-to-trim-on-each-side] |
| + | Alternately, the number of bases from each side can be specified (either or both -L/-R (--left/--right) can be specified): |
| + | ./bam trimBam [inFile] [outFile] -L [num-bases-to-trim-from-left] -R [num-bases-to-trim-from-right] |
| + | By default Left/Right is as the reads are in the SAM/BAM file. |
| + | |
| + | Optionally --reverse/-r can be specified to reverse the left/right for reverse reads |
| + | |
| + | trimBam will modify the sequences to 'N', and the quality string to '!' |
| | | |
| | | |
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| outFile : the SAM/BAM file to be written | | outFile : the SAM/BAM file to be written |
| num-bases-to-trim-on-each-side : the number of bases/qualities to trim from each side | | num-bases-to-trim-on-each-side : the number of bases/qualities to trim from each side |
| + | Instead of num-bases-to-trim-on-each-side, -L/-R can be specified to indicate the number of bases to trim from the left/right |
| + | Optional Parameters: |
| + | --reverse : reverse the left/right for reverse reads |
| </pre> | | </pre> |
| | | |
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| | | |
| = Example Output = | | = Example Output = |
| + | |
| + | If the number to trim from each side is the same: |
| + | <pre> |
| + | Arguments in effect: |
| + | Input file : testFiles/testSam.sam |
| + | Output file : results/trimSam.sam |
| + | #Bases to trim from each side : 2 |
| + | |
| + | Number of records read = 10 |
| + | Number of records written = 10 |
| + | </pre> |
| + | |
| + | If the number to trim from each side is different (but left/right is the same for forward/reverse): |
| <pre> | | <pre> |
| Arguments in effect: | | Arguments in effect: |
| Input file : testFiles/testSam.sam | | Input file : testFiles/testSam.sam |
| Output file : results/trimSam.sam | | Output file : results/trimSam.sam |
− | #TrimBases : 2 | + | #Bases to trim from the left of forward strands : 1 |
| + | #Bases to trim from the right of forward strands: 2 |
| + | #Bases to trim from the left of reverse strands : 1 |
| + | #Bases to trim from the right of reverse strands : 2 |
| | | |
| Number of records read = 10 | | Number of records read = 10 |
| Number of records written = 10 | | Number of records written = 10 |
| </pre> | | </pre> |
| + | |
| + | |
| + | If the number to trim from each side is different and the reverse option is used(left/right is opposite for reverse): |
| + | <pre> |
| + | Arguments in effect: |
| + | Input file : testFiles/testSam.sam |
| + | Output file : results/trimSam.sam |
| + | #Bases to trim from the left of forward strands : 1 |
| + | #Bases to trim from the right of forward strands: 2 |
| + | #Bases to trim from the left of reverse strands : 2 |
| + | #Bases to trim from the right of reverse strands : 1 |
| + | |
| + | Number of records read = 10 |
| + | Number of records written = 10 |
| + | </pre> |
| + | |
| | | |
| [[Category:BamUtil|trimBam]] | | [[Category:BamUtil|trimBam]] |
| [[Category:BAM Software]] | | [[Category:BAM Software]] |
| [[Category:Software]] | | [[Category:Software]] |