pysam alignment error I checked my bam files and they look fine How did you check and how did you conclude the files are fine?
[main_samview] fail to read the header from sample. bam - Biostar: S That's exactly the problem: The -U option is to Output reads not selected by filters to FILE, but the option you want is the -u to get Uncompressed BAM output, which already implies -b so you don't need to specify it Also, the -S option to indicate that your input is SAM rather than BAM is deprecated, but samtools doesn't complain if you use it
Dealing with nanopore fast5 files compressed with vbz - Biostar: S I spent quite a bit of effort troubleshooting this so I thought of posting it for my own reference and for the community benefit, hopefully Starting with MinKNOW (I think), Nanopore sequencing started producing fast5 files compressed with their vbz custom algorithm instead of gzip vbz compression means that any software handling the raw signal from these fast5 files will fail with more or
HTSeq error when reading BAM file - biostars Error occured when reading beginning of SAM BAM file file header is empty (mode='rb') - is it SAM BAM format? [Exception type: ValueError, raised in calignmentfile pyx:574]
How to fix: Error: No module named HTSeq. scripts? - biostars [Exception type: ValueError, raised in libcalignmentfile pyx:1000] I found a solution on the Internet: https: www seqanswers com forum bioinformatics bioinformatics-aa 9688-problem-using-htseq
Pysam is giving - ValueError: reference_id -1 out of range 0 lt;=tid lt;65334 . . . File "pysam calignmentfile pyx", line 663, in pysam calignmentfile AlignmentFile get_reference_name (pysam calignmentfile c:8913) ValueError: reference_id -1 out of range 0<=tid<65334 So, it is able to accept all the tids with values less than 65334 (only when using paired end reads)
What are the columns from pysam fetch? - Biostar: S You can see the code of the class here: https: github com pysam-developers pysam blob bd4b335f03583f150f1fd161af84a6ab2edb468b pysam libcalignedsegment pyx#L906 In particular, the code of AlignedSegment __str__() is here: https: github com pysam-developers pysam blob bd4b335f03583f150f1fd161af84a6ab2edb468b pysam libcalignedsegment pyx#L967
RseQC inner_distance. py error - Biostar: S I managed to get this working I think the issue is related to an imperfect BED file I downloaded a new BED file from UCSC using the GENCODE v23 track with the Basic table I then used cat hg38_GENCODE_v23_basic | sed "s ^chr " > hg38_GENCODE_v23_basic nochr bed to strip the leading chr marker that isn't used in my STAR-aligned BAM files Using that new BED file I was able to run inner
rMATS cant open bam created by hisat2 this is my list file and what's the problem can you tell me? Can rMATS open bam created by hisat2 instead of STAR?