User: martyferr90
martyferr90 • 30
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Comment:
C: Split BAM file from more sample
... Ok, now I have 94 bam files, but I have 11 sample, any idea to how can I have 1 file for sample? ...
written 3.1 years ago by
martyferr90 • 30
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Comment:
C: Split BAM file from more sample
... every RG is like this:
@RG ID:L7IZC.1 PL:IONTORRENT PU:s5/540 FO:TACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTA ...
written 3.1 years ago by
martyferr90 • 30
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Comment:
C: Split BAM file from more sample
... If so, should I not have 24*11 IDs? ...
written 3.1 years ago by
martyferr90 • 30
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Comment:
C: Split BAM file from more sample
... I tryed to convert my bam file into a sam file to understand something. The complete head is:
@HD VN:1.4 GO:none SO:coordinate
@RG ID:L7IZC PL:IONTORRENT PU:s5/540 FO:TACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTA ...
written 3.1 years ago by
martyferr90 • 30
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Comment:
C: Split BAM file from more sample
... this is the output
L7IZC:01332:11594 4 * 0 0 * * 0 0TAGAGAGTACGATCTCAGGTTTCAGGGTTATTTGACTACTACCTAGCTCAAGTCTTGAGCCACCATTACGTGTGCTAGAAAGGGTTACTAACCTCTGCCGAAGGGCTATAATGCTTACTGTAGAATTCTACTTGTCTATAGGATAAAGCATGATAATGGATGGTGGTAATTGCTCA <;;>6==4<;;;2=5:;;/98::;;;7/*//////7499::7<=;<655.4 ...
written 3.1 years ago by
martyferr90 • 30
• updated
3.1 years ago by
GenoMax ♦ 94k
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Comment:
C: Split BAM file from more sample
... I'm not sure that my txt file contain the RG tags, because in my files there are this information:
sample1.sorted.bam sample2.sorted.bam (and other 9)
14578326 10905678 9856227 14119725 12330675 1395283512191130 13570563 43751694 6531804 10925343
14551023 10883187 9835887 14095128 1 ...
written 3.1 years ago by
martyferr90 • 30
• updated
3.1 years ago by
GenoMax ♦ 94k
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... Hi all! I have a little problem: I have 1 bam file (44gb ca) ant it contain the reads from 11 different sample. I have 2 txt file with sample name and a lot tab delimited number.
How can I split this unique BAM file into 11 different bam files?
Is it correct to use the following code?
samtools vie ...
written 3.1 years ago by
martyferr90 • 30
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... the output is still pemission denied .-. ...
written 3.1 years ago by
martyferr90 • 30
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... -rw-r--r-- this are the permission of my 31 files in the directory of the path that I use in $(path_to_my_fastq_file).
If I type the command with only one file it works (simple bowtie 2 -x hg19 in.fastq | samtools sort -o out.bam), with a for instruction doesn't work anymore .-. ...
written 3.1 years ago by
martyferr90 • 30
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... Hi! I tryed your code, but my error is still: permission denied. Any idea? ...
written 3.1 years ago by
martyferr90 • 30
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