User: User000

gravatar for User000
User000270
Reputation:
270
Status:
Trusted
Location:
Last seen:
1 month ago
Joined:
5 years, 12 months ago
Email:
o********@gmail.com

about me

Posts by User000

<prev • 207 results • page 1 of 21 • next >
0
votes
0
answers
77
views
0
answers
Get the ID's for Paired-end Reads from BAM file including /1 and /2
... 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 ...
seqkit samtools written 4 weeks ago by User000270
0
votes
0
answers
202
views
0
answers
Comment: 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 User000270
0
votes
0
answers
202
views
0
answers
Comment: C: FASTQ exctract ID's
... if it was that easy, not all of them are hiseq1. ...
written 4 weeks ago by User000270
0
votes
0
answers
202
views
0
answers
Comment: 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 User000270
0
votes
0
answers
202
views
0
answers
Comment: 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 User000270
0
votes
0
answers
202
views
0
answers
Comment: 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 User000270
0
votes
0
answers
202
views
0
answers
Comment: 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 User000270
0
votes
0
answers
202
views
0
answers
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 User000270
0
votes
0
answers
202
views
0
answers
Comment: C: FASTQ exctract ID's
... thanks a lot, could you please specify what does -f do? ...
written 4 weeks ago by User000270
0
votes
0
answers
202
views
0
answers
Comment: C: FASTQ exctract ID's
... sorry, this isn't very clear form me, I will read the manual.. ...
written 4 weeks ago by User000270

Latest awards to User000

Great Question 16 months ago, created a question with more than 5,000 views. For Mapping Illumina reads against one single gene
Popular Question 16 months ago, created a question with more than 1,000 views. For Convert BLAST format to EMBL file format
Popular Question 16 months ago, created a question with more than 1,000 views. For Aligning BAC to an assembled sequence
Popular Question 16 months ago, created a question with more than 1,000 views. For A tool to align two assembled sequences
Popular Question 16 months ago, created a question with more than 1,000 views. For BAM file interpretation and consensus creation
Popular Question 16 months ago, created a question with more than 1,000 views. For Running BLAST on huge files
Popular Question 16 months ago, created a question with more than 1,000 views. For Mapping RNA-seq against genome
Popular Question 16 months ago, created a question with more than 1,000 views. For Download genes from KEGG pathway
Popular Question 19 months ago, created a question with more than 1,000 views. For Mapping RNA-seq against genome
Popular Question 19 months ago, created a question with more than 1,000 views. For Aligning BAC to an assembled sequence
Popular Question 22 months ago, created a question with more than 1,000 views. For Mapping RNA-seq against genome
Popular Question 22 months ago, created a question with more than 1,000 views. For Aligning BAC to an assembled sequence
Popular Question 22 months ago, created a question with more than 1,000 views. For Mapping RNA-seq against genome
Popular Question 23 months ago, created a question with more than 1,000 views. For Mapping RNA-seq against genome
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Aligning BAC to an assembled sequence
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Aligning BAC to an assembled sequence
Popular Question 2.3 years ago, created a question with more than 1,000 views. For BAM file interpretation and consensus creation
Popular Question 2.6 years ago, created a question with more than 1,000 views. For BAM file interpretation and consensus creation
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Finding Overlapping, Non Overlapping Hits
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Finding Overlapping, Non Overlapping Hits
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Finding Overlapping, Non Overlapping Hits
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Finding Overlapping, Non Overlapping Hits
Popular Question 3.7 years ago, created a question with more than 1,000 views. For Plant Annotation Workflow
Popular Question 3.8 years ago, created a question with more than 1,000 views. For Mapping Illumina reads against one single gene
Centurion 3.9 years ago, created 100 posts.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1513 users visited in the last hour