This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Extract Umi sequence to readname
@BH04640:4:22CNJJLT3:5:1101:27120:1048 1:N:0:CAAGGTGA+AGTCGCGA
GNACTGTTATCTATTGAAGGACATGTGCATTACCTTATACAGGAAGCTACTGATGAAAACTTACTATGCCAGATGTATCTTGGTTGGACTCCATATATGTGAAATGAAATTATGTAAAAGAATATGTTAAAGTAGAGATCGGAAGAGCAC
+
I#IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII

My sequence looks like this. I am trying to extract the umi sequence using FGBIO - FastqToBam tool. can anyone tell me How to Extract the UMI in ubam. Because when i run the FastqToBam the umis are not extracted

BH04640:4:22CNJJLT3:5:1101:27009:1048:CAAGGTGA+AGTCGCGA 4   *   0   0   *   *   0   0   CNAGTAGCTAGAGTGGTGGCACATGCCTGTAGTCCCAGCTACTCGGAAGGCTGAGGTGGGAGAATCACTTGAACTCAGGAGGCGGAGGTTGCAGTGAGCCGAGATTGCGCCACTGCACTCCAGCCTGGGAGACAGAGCAAGACTCTGCCT  I#IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII  RG:Z:A.

I also want to know the coressponding read structure for the sample given

sequence fgbio umi
• 908 views • link
updated by GenoMax GenoMax • written by Smilesky • Smilesky

0 answers

No answers yet.

Log in to answer this question.

More posts like this
  • DNA sequencing workflow involving UMIs
    written by ww22runner • ww22runner
    Hello everyone, I currently use a workflow for NGS without UMIs that looks like this upstream: a\. *Fastqs* b\. *Remove sequence adapters* c\. *Alignment using …
  • Removing umi split off as a separate fastq (RNA-seq)
    written by YJ • YJ
    Hi, I used x-gen udi/umi adaptors from idt to generate my RNA-seq samples and ran my single end RNA-seq experiment. I received two fastq files …
  • How to combine UMIs split across reads 1 and 2 into a single UMI for deduplication?
    written by SethG • SethG
    I am building small RNA libraries designed like this: [5' adapter]-[6N umi] --- [insert] --- [6N umi]-[3' adapter] I collect paired end data but map …
  • AssertionError: not all umis are the same length(!): 4 - 5
    written by monalisa6hota • monalisa6hota
    Hello, I am trying to run UMI-tools to remove duplicated reads based on UMI. But getting error "AssertionError: not all umis are the same length(!): …
  • umi_tools using regex greedy quantifiers only returning 1 character
    written by williamtmills • williamtmills
    I am trying to use umi_tools to remove UMIs and cell barcodes and leave the remaining sequence. Unfortunately, after correctly removing the umi and cell …
  • How to cut some part of the header of reads in FASTQ file?
    written by naeem40thju • naeem40thju
    The head of reads contains long characters. Actually I wanted to use UMI-tools. If I extract UMI and add to the header ('_' separated), it …
  • Bulk RNA-Seq pipeline suggestion incorporating UMIs
    written by steveh • steveh
    Hi, I have 149 bulk RNA-Seq samples (100 bp, paired-end, Illumina) which have come from sequencing in the form of fastq **triplets**, i.e. pairs of …
  • Tutorial: Use fastp to preprocess FASTQ data with unique molecular identifer (UMI) integrated
    written by chen chen
    fastp (https://github.com/OpenGene/fastp) is an open source tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported …
  • Extract the DNA sequence header!
    written by fufuyou fufuyou
    I have question about our DNA sequence data. If the format of sequence data is ``` @HWI-ST1234:136:C5F6VACXX:6:1101:4121:2231 1:N:0:ACTTGA TATGGGTTTCCACGGAGCACAGTGCCTAGTGCTCACTCCCCAGTTGTATCTTATTTTTCAGGTCAGCAGGTCGGGCCGGGAGTGTGACATGACGGAGCAGA + CCCFFFDDHHHHHJJGIJJJJJHIJJIJJHIJIJIJJJJJJIIIIJGIIBFHHFHJJJG>FHIJIGIIEHAHBBAB@BDBDD<?ACA>CDDDDDD5<BBD?. ``` I can extract …
  • searching reads with a certain sequence in fastq file
    written by sumithrasank75 sumithrasank75
    I have a file say master.fastq which looks like : ``` @M00990:202:000000000-ADM27:1:1101:21678:1536 2:N:0:291 CCTTTTACCGACCCGCTCTTTCTCTCCTACGCTTATTTCCGTCTACCCTTCTCTTCACTCGCTATTTCTATTCTTAAAACTATCTTAATGTTCTGCCTTTGCTCTTTTCTTTTTTCTATAACCTCTCTACAGCCAACTCACCCATCTCCTTCCCTGCTACGCTATTCCTCTGTTAGTTTTTCTTCATCATACTTTTCTCATCTCACACTACCTTTGCACTTCTTCCTTTCCACGTCCCCTTTCTCCTACC + -----,,6;6,@+8++6+,,,<C5@,,,,,,+8,,;,,<,,,,,,,;,,;,,,<C,,,;,,8,,8CC,C,,,5,C,,,,99,+,+4,,,3,,9,,6,@<,,,,,,,9,,,,,,,4),,0**,,5),,5**,)59*0),,*)5,)))*,9,3,0++))5D:)))))5;+;+0)*;+*6++++),******3**50,6,+++**,0*,,31)88*0*1*5*1)0*:*7>C;3,035:0)))8).*2**.*:) @M00990:202:000000000-ADM27:1:1101:22685:1539 2:N:0:291 CTTATCACCGACTCTCTCCTTCTCTTCCAAGTTTATTTCCGACTCCCCTTATCTTCACTTGCTATTTCTATTCTTAAAACTATCTCGACCTTTCACCTTTCCCTCTTTCCTTCTTTTCTCTCCTTCTACACTCCCACCCACTCTTACTTCTTTCTTGTCACCGTTTCCATATTATACTTTCTTCTCTTACATAATTTTCTTCCTGCAAACTATTTAAGCAATCTCTTTCTTTCACCCCTTTTATCTCGCC + -----,,<;67@+B,,6,,,,;C5@,,,,,66<,,6,,<,,,66,,;,66,,;;C,,,;,4<,,<CC6C,;,,,;,,6,:,6?A9=,,+++2,5,,,9<?D,,,,,:C?,@,@,,5,?*3*,9**,,0**,*)93))4+))19*0**,,52,56+**5*03*)3)))42+2***5*+=3+,*4*2****,**2*,3,+++*0,50,,**5*****0****)5)***0**,,***3*)0)))3***0*))) ``` I want only …