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| Alternately, the number of bases from each side can be specified (either or both -L/-R (--left/--right) can be specified): | | 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] | | ./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 | + | By default reverse strands are reversed and then the left & right are trimmed. |
| + | |
| + | This means that --left actually trims from the right of the read in the SAM/BAM for reverse reads. |
| + | |
| + | Optionally --ignoreStrand/-i can be specified to ignore the strand information and treat forward/reverse the same. |
| | | |
| trimBam will modify the sequences to 'N', and the quality string to '!' | | trimBam will modify the sequences to 'N', and the quality string to '!' |
| + | |
| | | |
| = Parameters = | | = Parameters = |
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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 (or --left/--right) can be specified to indicate the number of bases to trim from the left/right | + | Instead of num-bases-to-trim-on-each-side, -L/-R (or --left/--right) can be specified to indicate the number of bases to trim from the left/right (left/right are reversed for reverse strands) |
| Optional Parameters: | | Optional Parameters: |
− | --reverse : reverse the left/right for reverse reads | + | --ignoreStrand : ignore strand information - do not reverse left/right for reverse reads |
| </pre> | | </pre> |
| | | |
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| </pre> | | </pre> |
| | | |
− | ==Trim different bases from each side, but treat forward & reverse the same== | + | |
− | Example Input, trimming 1 base from the left and 2 bases from the right: | + | ==Trim different bases from each side, but treat reverse strands the opposite== |
| + | Example Input, trimming 1 base from the left and 2 bases from the right for forward strands and do the opposite for reverse strands: |
| <pre> | | <pre> |
| ./bin trimBam testFiles/testSam.sam results/trimSam.sam -L 1 -R 2 | | ./bin trimBam testFiles/testSam.sam results/trimSam.sam -L 1 -R 2 |
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| #Bases to trim from the left of forward strands : 1 | | #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 right of forward strands: 2 |
− | #Bases to trim from the left of reverse strands : 1 | + | #Bases to trim from the left of reverse strands : 2 |
− | #Bases to trim from the right of reverse strands : 2 | + | #Bases to trim from the right of reverse strands : 1 |
| | | |
| Number of records read = 10 | | Number of records read = 10 |
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| | | |
| | | |
− | ==Trim different bases from each side, but treat reverse strands the opposite== | + | ==Trim different bases from each side, but treat forward & reverse the same== |
− | Example Input, trimming 1 base from the left and 2 bases from the right for forward strands and do the opposite for reverse strands: | + | Example Input, trimming 1 base from the left and 2 bases from the right ignoring strand information: |
| <pre> | | <pre> |
− | ./bin trimBam testFiles/testSam.sam results/trimSam.sam -L 1 -R 2 --reverse | + | ./bin trimBam testFiles/testSam.sam results/trimSam.sam -L 1 -R 2 --ignoreStrand |
| </pre> | | </pre> |
| Example Output: | | Example Output: |
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| #Bases to trim from the left of forward strands : 1 | | #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 right of forward strands: 2 |
− | #Bases to trim from the left of reverse strands : 2 | + | #Bases to trim from the left of reverse strands : 1 |
− | #Bases to trim from the right 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> |
| + | |
| | | |
| | | |