From Genome Analysis Wiki
Jump to navigationJump to search
24 bytes removed
, 19:39, 9 December 2014
Line 81: |
Line 81: |
| If you want to check if you still have the bam index file, run | | If you want to check if you still have the bam index file, run |
| | | |
− | head ${OUT}/bam.index | + | head ${OUT}/bam.list |
| | | |
| <ul> | | <ul> |
Line 87: |
Line 87: |
| <li>View Results</li> | | <li>View Results</li> |
| <div class="mw-collapsible-content" style="width:800px"> | | <div class="mw-collapsible-content" style="width:800px"> |
− | HG00641 ALL /net/seqshop-server/hmkang/out/bams/HG00641.recal.bam | + | HG00641 /net/seqshop-server/home/hmkang/out/bams/HG00641.recal.bam |
− | HG00640 ALL /net/seqshop-server/hmkang/out/bams/HG00640.recal.bam | + | HG00640 /net/seqshop-server/home/hmkang/out/bams/HG00640.recal.bam |
− | HG00551 ALL /net/seqshop-server/hmkang/out/bams/HG00551.recal.bam | + | HG00551 /net/seqshop-server/home/hmkang/out/bams/HG00551.recal.bam |
− | HG00553 ALL /net/seqshop-server/hmkang/out/bams/HG00553.recal.bam | + | HG00553 /net/seqshop-server/home/hmkang/out/bams/HG00553.recal.bam |
− | HG00554 ALL bams/HG00554.recal.bam | + | HG00554 bams/HG00554.recal.bam |
− | HG00637 ALL bams/HG00637.recal.bam | + | HG00637 bams/HG00637.recal.bam |
− | HG00638 ALL bams/HG00638.recal.bam | + | HG00638 bams/HG00638.recal.bam |
− | HG00734 ALL bams/HG00734.recal.bam | + | HG00734 bams/HG00734.recal.bam |
− | HG00736 ALL bams/HG00736.recal.bam | + | HG00736 bams/HG00736.recal.bam |
− | HG00737 ALL bams/HG00737.recal.bam | + | HG00737 bams/HG00737.recal.bam |
| </div> | | </div> |
| </div> | | </div> |
Line 103: |
Line 103: |
| Also, make sure that you have only 62 samples (you did not append new files twice) | | Also, make sure that you have only 62 samples (you did not append new files twice) |
| | | |
− | wc -l ${OUT}/bam.index | + | wc -l ${OUT}/bam.list |
| | | |
| Your expected output is similar to this. | | Your expected output is similar to this. |
| | | |
− | 62 /net/seqshop-server/hmkang/out/bam.index | + | 62 /net/seqshop-server/hmkang/out/bam.list |
| | | |
| === Reference Files === | | === Reference Files === |