User: martyferr90

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martyferr9030
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Posts by martyferr90

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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 2.1 years ago by martyferr9030
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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 2.1 years ago by martyferr9030
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Comment: C: Split BAM file from more sample
... If so, should I not have 24*11 IDs? ...
written 2.1 years ago by martyferr9030
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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 2.1 years ago by martyferr9030
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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 2.1 years ago by martyferr9030 • updated 2.1 years ago by genomax76k
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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 2.1 years ago by martyferr9030 • updated 2.1 years ago by genomax76k
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Split BAM file from more sample
... 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 ...
sample split bam bam split written 2.1 years ago by martyferr9030
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Comment: C: Multiple fastq alignment with bowtie2
... the output is still pemission denied .-. ...
written 2.1 years ago by martyferr9030
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Comment: C: Multiple fastq alignment with bowtie2
... -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 2.1 years ago by martyferr9030
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Comment: C: Multiple fastq alignment with bowtie2
... Hi! I tryed your code, but my error is still: permission denied. Any idea? ...
written 2.1 years ago by martyferr9030

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