Body: <p>I have RNA seq data of 12 samples (paired end, so 24 files)  and I ran tophat2 for alignment on all of them which gave me one bam file for all the samples. Now I need separate bam files for all the samples. Can I spilt them from the one I have or I have to do tophat2 for all the samples separately? If yes, how to do it.</p>
  <p>I need them for FRASER (splicing detction) I would also appreciate if anyone used FRASER before could help me a bit to get started. I am working with plant data for the first time.</p>
  <p>The command I used</p>
  <pre><code>tophat2 -p 40 \
      -o tophat_output_final bowtie_indexes/Medicago1/Medicago \
      NRNSA_S103_R1_001.fastq.gz,NRNSB_S107_R1_001.fastq.gz,\
        NRNSC_S111_R1_001.fastq.gz,NRSA_S104_R1_001.fastq.gz,\
        NRSB_S108_R1_001.fastq.gz,NRSC_S112_R1_001.fastq.gz,\
        RNSA_S105_R1_001.fastq.gz,RNSB_S109_R1_001.fastq.gz,\
        RNSC_S113_R1_001.fastq.gz,SRAB_S106_R1_001.fastq.gz,\
        SRB_S110_R1_001.fastq.gz,SRC_S114_R1_001.fastq.gz \
      NRNSA_S103_R2_001.fastq.gz,NRNSB_S107_R2_001.fastq.gz,\
        NRNSC_S111_R2_001.fastq.gz,NRSA_S104_R2_001.fastq.gz,\
        NRSB_S108_R2_001.fastq.gz,NRSC_S112_R2_001.fastq.gz,\
        RNSA_S105_R2_001.fastq.gz,RNSB_S109_R2_001.fastq.gz,\
        RNSC_S113_R2_001.fastq.gz,SRAB_S106_R2_001.fastq.gz,\
        SRB_S110_R2_001.fastq.gz,SRC_S114_R2_001.fastq.gz
  </code></pre>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-08-14T18:40:42.640Z
Comments.Text: Did you assign read groups while aligning? Can you add the command that you used with tophat2?
Comments.UserDisplayName: Wouter De Coster
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-08-16T02:08:57.703Z
Comments.Text: Hi Wouter De Coster, I have added the command in the question itself. I don't know what you mean by assigning read groups?
Comments.UserDisplayName: Dixi Modi
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-08-16T18:06:02.647Z
Comments.Text: The way you aligned them you can not split them in separate samples. You should have run Tophat2 for each sample separately.
Comments.UserDisplayName: Wouter De Coster
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-08-17T01:53:36.753Z
Comments.Text: Thank you, Wouter De Coster I have 3 replicates of each treatment. so 4 treatments x 3 replicates =12 files.
  
  Should I merge the replicates or just go for separate alignment for each sample?
Comments.UserDisplayName: Dixi Modi
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-08-17T19:22:39.900Z
Comments.Text: Yes, separate alignments for each (biological) replicate
Comments.UserDisplayName: Wouter De Coster
Tags: <rna-seq><sam><multiple-sequence-alignment>
Title: Splitting .bam files into separate samples for tophat2
ThreadText: # Splitting .bam files into separate samples for tophat2
  
  (Asked by: username_0 on 2021-08-14)
  
  I have RNA seq data of 12 samples (paired end, so 24 files) and I ran tophat2 for alignment on all of them which gave me one bam file for all the samples. Now I need separate bam files for all the samples. Can I spilt them from the one I have or I have to do tophat2 for all the samples separately? If yes, how to do it.
  
  I need them for FRASER (splicing detction) I would also appreciate if anyone used FRASER before could help me a bit to get started. I am working with plant data for the first time.
  
  The command I used
  
  ```
  tophat2 -p 40 \
      -o tophat_output_final bowtie_indexes/Medicago1/Medicago \
      NRNSA_S103_R1_001.fastq.gz,NRNSB_S107_R1_001.fastq.gz,\
        NRNSC_S111_R1_001.fastq.gz,NRSA_S104_R1_001.fastq.gz,\
        NRSB_S108_R1_001.fastq.gz,NRSC_S112_R1_001.fastq.gz,\
        RNSA_S105_R1_001.fastq.gz,RNSB_S109_R1_001.fastq.gz,\
        RNSC_S113_R1_001.fastq.gz,SRAB_S106_R1_001.fastq.gz,\
        SRB_S110_R1_001.fastq.gz,SRC_S114_R1_001.fastq.gz \
      NRNSA_S103_R2_001.fastq.gz,NRNSB_S107_R2_001.fastq.gz,\
        NRNSC_S111_R2_001.fastq.gz,NRSA_S104_R2_001.fastq.gz,\
        NRSB_S108_R2_001.fastq.gz,NRSC_S112_R2_001.fastq.gz,\
        RNSA_S105_R2_001.fastq.gz,RNSB_S109_R2_001.fastq.gz,\
        RNSC_S113_R2_001.fastq.gz,SRAB_S106_R2_001.fastq.gz,\
        SRB_S110_R2_001.fastq.gz,SRC_S114_R2_001.fastq.gz
  
  ```
  
  **Tags:** rna-seq, sam, multiple-sequence-alignment
  
  > **Comments:**
  > **username_1**: Did you assign read groups while aligning? Can you add the command that you used with tophat2?  
  > **username_0**: Hi username_1 De username_1, I have added the command in the question itself. I don't know what you mean by assigning read groups?  
  > **username_1**: The way you aligned them you can not split them in separate samples. You should have run Tophat2 for each sample separately.  
  > **username_0**: Thank you, username_1 De username_1 I have 3 replicates of each treatment. so 4 treatments x 3 replicates =12 files.  Should I merge the replicates or just go for separate alignment for each sample?  
  > **username_1**: Yes, separate alignments for each (biological) replicate  
  
  ---
  
  ## 0 answers
  
  