User: User000
User000 • 270
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... Hello,
I want to extract the ID's from a BAM file and I use the following command line:
samtools view {input.unmerged} | cut -f 1 | awk '!x[$0]++' > {output.txt}
This is the output.txt,
HISEQ1:105:C0A57ACXX:2:1105:12172:84568
HISEQ1:105:C0A57ACXX:2:1108:17762:41110
Now, I actually ...
written 4 weeks ago by
User000 • 270
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C: FASTQ exctract ID's
... I have many bam files, it was just an example. The problem is that you guys don't try to read and UNDERSTAND the question. I guess it is clear I have ID's from BAM and trying to get them their FASTQ. Anyway grep o parse would not solve the problem from biological point pf view. I will get only one o ...
written 4 weeks ago by
User000 • 270
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C: FASTQ exctract ID's
... if it was that easy, not all of them are hiseq1. ...
written 4 weeks ago by
User000 • 270
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C: FASTQ exctract ID's
... moreover, if we do grep '@' it is going to grep also some quality values in the lines below... ...
written 4 weeks ago by
User000 • 270
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C: FASTQ exctract ID's
... I thank you very much for trying to help me. I try to explain better: LET'S SAY, I have 2 BAM files each with unmapped reads. I extracted the ID's of the reads in those 2 BAM files and compared the list and got the ID list that is present in BAM 1 but not BAM 2. Now I want to extract the FASTQ of th ...
written 4 weeks ago by
User000 • 270
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C: FASTQ exctract ID's
... having the list of my reads and bam files that were transformed in fastq (of course my list of reads has only some IDs,not all present in the fastq file), I want to extract the fastq's of the reads that I have in my list.... but since i have /1 and /2 It is empty... I am guessing I should transform ...
written 4 weeks ago by
User000 • 270
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C: FASTQ exctract ID's
... ok...and I nedd to extract the reads ID's I have above from the BAM file? I mean both R1 and R2 ...
written 4 weeks ago by
User000 • 270
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Comment:
C: FASTQ exctract ID's
... yes, unmapped reads... none of the replies above resolve my problem because I have this /1 and /2 in my fastq file... ...
written 4 weeks ago by
User000 • 270
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Comment:
C: FASTQ exctract ID's
... thanks a lot, could you please specify what does -f do? ...
written 4 weeks ago by
User000 • 270
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Comment:
C: FASTQ exctract ID's
... sorry, this isn't very clear form me, I will read the manual.. ...
written 4 weeks ago by
User000 • 270
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